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Deleted in azoospermia-like ( DAZL ) is essential for mammalian testicular function and spermatogenesis. To explore the molecular characterization, expression patterns, and cellular localization of the DAZL in Hezuo pig testes, testicular tissue was isolated from Hezuo pig at five development stages including 30 days old (30 d), 90 days old (90 d), 120 days old (120 d), 180 days old (180 d), and 240 days old (240 d). DAZL cDNA was first cloned using the RT-PCR method, and its molecular characterization was analyzed using relevant bioinformatics software. Subsequently, the expression patterns and cellular localization of DAZL were evaluated using quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry. The cloning and sequence analysis showed that the Hezuo pig DAZL cDNA fragment contained 888 bp open reading frame (ORF) capable of encoding 295 amino acid residues and exhibited high identities with some other mammals. The qRT-PCR and Western blot results indicated that DAZL was specifically expressed in Hezuo pig testes, and DAZL levels of both mRNA and protein were expressed at all five reproductive stages of Hezuo pig testes, with extremely significant higher expression levels in 90 d, 120 d, 180 d, and 240 d than those in 30 d ( p  < 0.01). Additionally, immunohistochemistry results revealed that DAZL protein was mainly localized in gonocytes at 30 d testes, primary spermatocytes, and spermatozoon at other developmental stages, and Leydig cells throughout five development stages. Together, these results suggested that DAZL may play an important role by regulating the proliferation or differentiation of gonocytes, development of primary spermatocytes and spermatozoon, and functional maintenance of Leydig cells in testicular development and spermatogenesis of Hezuo pig. Nevertheless, the specific regulatory mechanisms underlying these phenomena still requires further investigated and verified.

1. NOD1 is a significant member of the NOD-like receptor (NLR) family. Its main role is to identify microorganisms that invade the body, transmit immune signals and regulate innate immune responses. However, the expression and role of the NOD1 in immune defence against infection in geese remain unknown.2. The RT-PCR method and rapid amplification of cDNA ends (RACE) was used to obtain the full-length goose NOD1 ( gNOD1 ) cDNA series. The cDNA for gNOD1 contains 2856-bp nucleotides, i.e . 47-bp 5' UTR, 135-bp 3' UTR, and 1275-bp ORF region, and encodes a 951-amino-acids (AAs) polypeptide chain. The nucleotide sequence of gNOD1 was found more than 90% similar to its homologs from other avian organisms.3. The qRT-PCR results showed that gNOD1 mRNA was widely distributed in different tissues, but highly expressed in liver, spleen, lung and caecum tissues.4. Following stimulation of goose embryo fibroblasts (GEFs) with lipopolysaccharide (LPS) and polyriboinosinic polyribocytidylic acid (poly(I:C)), the expression of gNOD1 and cytokines, such as IL-1β, IL-6, IL-18, and TNF-α, changed with the response-efficacy correlation at 24 and 48 h post-infection (hpi).5. When the goslings were challenged with Salmonella entertidis (SE) and LPS, the expression of gNOD1 was up-regulated at 3 and 6 hpi in the spleen and caecum tissues, respectively. However, after SE infection, the expression level of gNOD1 fluctuated, while in the LPS group, gNOD1 mRNA increased immediately at a peak time of 6 hpi and then steadily declined. These results indicated that NOD1 was associated with the potency to resist bacterial and viral infections in the goose, both in vivo and in vitro .

Toll-like receptors (TLRs) play an important role in detecting pathogen-associated molecular patterns (PAMPs). Among the TLRs, TLR7 is involved in the recognition of antiviral compounds and single-stranded RNA. This study was designed to explore the structure and function of TLR7 in duck ( Anas platyrhynchos ), a natural host for avian influenza virus. Firstly, the full-length cDNA of Shaoxing egg-laying duck TLR7 (duTLR7) was obtained using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). It consisted of 38 base pairs (bp) 5'-untranslated region (UTR), 187 bp 3'-UTR, and 3270 bp open reading frame that encodes a single protein of 1089 amino acid residues. DuTLR7 shares high identity with TLR7 genes from other vertebrates. In healthy ducks, duTLR7 transcripts were broadly expressed in different tissues, with higher expression levels in the liver, kidney, and thymus. The highest relative transcript level of duTLR7 could be induced with R848 stimulation. In addition, overexpression of duTLR7 by stimulating with poly(I:C) significantly promoted IFN-β, NF-κB, IRF7, TRIF, Mx, STAT1 and STAT2 expressions. Taken together, these results suggest that TLR7 may play an important role in the innate immune response of ducks.

This study aimed to develop an effective therapy against M2 macrophages and to investigate the effects of imidazole and mannose modified carboxymethyl chitosan-nanoparticles (MIC-NPs) on tumor growth and antitumor immune responses. MIC-NPs were constructed and analyzed through 1 H NMR, nano-laser particle size analyzer, and transmission electron microscopy. The nanoparticles were mainly distributed in 75-85 nm, and zeta potential was 1.5 mV. Cytotoxicity studies in vitro and in vivo indicated that MIC-NPs were safe. The targeting effect of MIC-NPs on M2 macrophages was observed through fluorescence microscope and microplate system. The results demonstrated the uptake of a large amount of FITC-loaded MIC-NPs by M2. Cell growth inhibition experiments showed that MIC-NPs significantly inhibited M2 through cell apoptosis. The evaluation of anti-tumor activity in vivo showed that MIC-NPs could accumulate in the tumor site to exert an anti-tumor effect. Flow cytometry showed that the proportion of M2 macrophages at the tumor site in the experimental group was significantly lower than that in the control group, while the Treg cells and cytotoxic T cells (CTL) were found to be increased. PCR detection showed that the cDNA of FIZZ, MR, TGF-β, and arginase, closely related to M2 macrophages, in the experimental group, was significantly lower than that in the control group, but there was no significant difference in the cDNA of Treg cell characteristic Foxp3 between the two groups. These results suggest that MIC-NPs are expected to provide a new and effective treatment for tumor.

The aim of this study was to investigate effects of dietary supplementation of resveratrol on immunity, antioxidative capacity, intestinal barrier function in weaning piglets. Here, fifty-four 28-day-old Duroc × Landrace × Yorkshire weaning piglets were randomly divided into three dietary treatments and fed with a basal diet or a basal diet supplemented with 150 and 300 mg/kg resveratrol, respectively, for 42 days. The results indicated that resveratrol increased serum immunoglobulin G content. In serum, resveratrol increased glutathione peroxidase enzyme activity and decreased malondialdehyde (MDA) content. In liver, resveratrol not only increased T-AOC and total superoxide dismutase enzyme activities but also decreased MDA content. Meanwhile, the results showed that resveratrol had significantly increased the jejunum villus height and villus height/crypt depth, and decreased the crypt depth in jejunum. Furthermore, the mRNA expressions of IL-10 and ZO-1 were significantly increased in jejunal mucosa. However, there was no significant difference in the mRNA expressions of TNF-α , IL-1β , IL-6 , Occludin and Claudin1 between the treatment groups and the control group. Taken together, these results indicated that dietary supplementation of resveratrol could increase antioxidant activity, promote the integrity of intestinal barrier and increase the production of anti-inflammatory cytokines in weaning piglets.

This paper aims to study the effect of the dietary treatments on mRNA expression of urea transporter B (UT-B) and some aquaporins (AQP) in rumen epithelium of Italian Simmental young bulls. Eighty animals allocated to 16 pens were fed from about 500 to 650 kg body weight with four experimental diets, which resulted from the combination of two crude protein levels (125 and 110 g/kg dry matter, diets M and L, respectively) and two nitrogen sources (soybean meal (SBM) or SBM partly replaced by an isonitrogenous mixture of corn and urea; diets -U and +U, respectively). At slaughtering samples of blood and rumen epithelium were collected from six bulls for each diet. Blood samples were analysed for haematological parameters and quantitative PCR was carried out on the mRNA extracted from the rumen epithelium samples. The bulls fed diets M had lower plasma concentrations of aspartate aminotransferase than those receiving diets L (78.9 vs. 88.3 U/l, p = 0.04). Plasma urea was higher (p = 0.03) for diets M and lower for diets +U (2.0 vs. 2.5 and 1.73 vs. 2.00 mmol/l, respectively, in M and L diets, p = 0.04). The effect of dietary treatments on rumen UT expression were limited to AQP3, which was down regulated (p = 0.01) in diets +U. Finally, a high positive correlation (R 2  = 0.871) between the expressions of AQP7 and AQP10 was found. In conclusion, the AQP3 appears very responsive to dietary treatments and therefore it is a candidate to be further studied in rumen metabolism experiments. The close relationship between mRNA expression of AQP7 and AQP10 indicates a similar function of these two proteins.

Purpose: To study gene expression modulation in response to continuous whole-body exposure to low-dose-rate gamma radiation and improve our understanding of the mechanism of this impact at the molecular basis., Materials and Methods: cDNA microarray method with complete pooling of samples was used to study expression changes in the transcriptome profile of livers from rats treated with prolonged low-dose-rate ionizing radiation (IR) relative to that of sham-irradiated rats., Results: Of the 209 genes that were two-fold-up or down-regulated, 143 were known genes of which 27 were found in previous literatures to be modulated by IR. Remarkably, there were a significant number of differentially expressed genes involved in hepatic lipid metabolism., Conclusion: This study showed changes in transcriptome profile of livers from low-dose irradiated rats when compared with that of sham-irradiated ones. This study will be useful for studying the metabolic changes of human exposed for long term to cosmic ray such as in space and in polar regions.

1. In a previous study, a laying-related single nucleotide polymorphism (SNP) Record-106975 (A-G) was found in the intron of Membrane-associated Guanylate Kinase with Inverted Domain Structure-1 (MAGI1) gene by restriction site-associated DNA sequencing. This study was performed to further identify the function of MAGI1 on laying performance in Yangzhou geese. 2. The complete MAGI1 cDNA sequence was cloned from the ovary of the Yangzhou goose. A total of 4 alternative splice variants were identified, and the characterisation of their nucleic acid and amino acid (AA) sequences were analysed. The AA sequence of goose MAGI1 was highly conserved with other avian species. 3. MAGI1 was ubiquitously expressed in 11 tested tissues, with greater amounts of mRNA in the granulosa cell layer and ovary. GG (n = 14) and GA (n = 6) genotypes of SNP Record-106975 showed significantly lower MAGI1 mRNA levels than those of the AA genotype. 4. Over-expression and knockdown experiments revealed that MAGI1 mRNA expression was associated with caspase-3 mRNA levels in granulosa cells, and may play a role in regulating apoptosis of granulosa cells.

Macroautophagy/autophagy plays a critical role in immunity by directly degrading invading pathogens such as Group A Streptococcus (GAS), through a process that has been named xenophagy. We previously demonstrated that autophagic vacuoles directed against GAS, termed GAS-containing autophagosome-like vacuoles (GcAVs), use recycling endosomes (REs) as a membrane source. However, the precise molecular mechanism that facilitates the fusion between GcAVs and REs remains unclear. Here, we demonstrate that STX6 (syntaxin 6) is recruited to GcAVs and forms a complex with VTI1B and VAMP3 to regulate the GcAV-RE fusion that is required for xenophagy. STX6 targets the GcAV membrane through its tyrosine-based sorting motif and transmembrane domain, and localizes to TFRC (transferrin receptor)-positive punctate structures on GcAVs through its H2 SNARE domain. Knockdown and knockout experiments revealed that STX6 is required for the fusion between GcAVs and REs to promote clearance of intracellular GAS by autophagy. Moreover, VAMP3 and VTI1B interact with STX6 and localize on the TFRC-positive puncta on GcAVs, and are also involved in the RE-GcAV fusion. Furthermore, knockout of RABGEF1 impairs the RE-GcAV fusion and STX6-VAMP3 interaction. These findings demonstrate that RABGEF1 mediates RE fusion with GcAVs through the STX6-VAMP3-VTI1B complex, and reveal the SNARE dynamics involved in autophagosome formation in response to bacterial infection.

Insulin-like growth factor-I (IGF-I) and myostatin (MSTN) are a pair of critical positive and negative growth regulators. The aim of the current study was to examine the age-dependent and muscle-specific expression of IGF-I and MSTN mRNAs in black Muscovy ducks in order to understand their roles in regulating the postnatal muscle growth of domestic ducks. The full-length cDNA of the black Muscovy duck MSTN gene was cloned and the age-dependent mRNA expression profile was compared with that of the IGF-I mRNA in skeletal muscles. The cDNA sequence of the MSTN gene was 1128 bp in length and encodes 375 amino acids, with more than 94.9% homology with poultry MSTN genes, and 83.0-92.0% homology with that of human and mammals (accession: KR006339.1). The IGF-I and MSTN mRNA expression exhibited opposite trends in age-dependency and in different muscles: IGF-I mRNA level was high in the early postnatal stage and low in the late mature stage, corresponding positively to growth; while the MSTN mRNA was low in the early stage, increased gradually and reached the highest level in mature muscles, and was negatively related to muscle growth. In the breast muscles, IGF-I mRNA was much higher than in the leg muscles; the opposite effect was seen in MSTN mRNA. These data suggest that the relative expression levels of IGF-I and MSTN are essential determinants in the temporal and muscle-specific regulation of postnatal skeletal muscle growth in Muscovy duck and possibly in other poultry species as well.

FYCO1 (FYVE and coiled-coil domain containing 1) functions as an autophagy adaptor in directly linking autophagosomes with the microtubule-based kinesin motor, and plays an essential role in the microtubule plus end-directed transport of autophagic vesicles. The specific association of FYCO1 with autophagosomes is mediated by its interaction with Atg8-family proteins decorated on the outer surface of autophagosome. However, the mechanistic basis governing the interaction between FYCO1 and Atg8-family proteins is largely unknown. Here, using biochemical and structural analyses, we demonstrated that FYCO1 contains a unique LC3-interacting region (LIR), which discriminately binds to mammalian Atg8 orthologs and preferentially binds to the MAP1LC3A and MAP1LC3B. In addition to uncovering the detailed molecular mechanism underlying the FYCO1 LIR and MAP1LC3A interaction, the determined FYCO1-LIR-MAP1LC3A complex structure also reveals a unique LIR binding mode for Atg8-family proteins, and demonstrates, first, the functional relevance of adjacent sequences C-terminal to the LIR core motif for binding to Atg8-family proteins. Taken together, our findings not only provide new mechanistic insight into FYCO1-mediated transport of autophagosomes, but also expand our understanding of the interaction modes between LIR motifs and Atg8-family proteins in general.

Mothers against decapentaplegic homolog 4 (SMAD4) is an important protein in animal reproduction. It plays pivotal roles in cellular pathways, including apoptosis. The expression profile of the SMAD4 gene in goose ovarian follicles has not been reported. In this study, the SMAD4 coding sequence was cloned from the Yangzhou goose. A phylogenetic analysis was performed and mRNA expression was examined in various tissues using quantitative real-time PCR. An alternative splice form of SMAD4, SMAD4-b having 1656 bp, was identified. SMAD4-a mRNA was widely expressed in various healthy tissues, whereas SMAD4-b was very weakly expressed. SMAD4 mRNA in the ovary and oviduct was significantly higher than that in the pituitary and hypothalamus. SMAD4 mRNA expression analysis in hierarchical follicles showed that the level of SMAD4 mRNA was higher in large white follicles and post-ovulatory follicles than in the other follicles. The results indicate that SMAD4 might be involved in the recruitment of hierarchical follicles.

Agouti signalling protein (ASIP) is an endogenous antagonist of melanocortin-1 receptor (MC1R) and is involved in the regulation of pigmentation in mammals. The objective of this study was to identify and characterise the ASIP gene in domestic goose. The goose ASIP cDNA consisted of a 44-nucleotide 5'-terminal untranslated region (UTR), a 390-nucleotide open-reading frame (ORF) and a 45-nucleotide 3'-UTR. The length of goose ASIP genomic DNA was 6176 bp, including three coding exons and two introns. Bioinformatic analysis indicated that the ORF encodes a protein of 130 amino-acid residues with a molecular weight of 14.88 kDa and an isoelectric point of 9.73. Multiple sequence alignments and phylogenetic analysis showed that the amino-acid sequence of ASIP was conserved in vertebrates, especially in the avian species. RT-qPCR showed that the goose ASIP mRNA was differentially expressed in the pigment deposition tissues, including eye, foot, feather follicle, skin of the back, as well as in skin of the abdomen. The expression level of the ASIP gene in skin of the abdomen was higher than that in skin of the back. Those findings will contribute to further understanding the functions of the ASIP gene in geese plumage colouring.

1. The Forkhead box O3 (FOXO3) transcription factor is a crucial regulator of cell fate that controls proliferation, apoptosis and differentiation. However, the role of FOXO3 regulation in duck myoblasts is not fully understood. 2. The aim of this study was to clone and determine the complete coding sequence (CDS) of the duck FOXO3 gene and to assess its function in myoblasts. 3. Primers specific for the predicted duck FOXO3 gene were designed using the public mallard duck reference sequence in GenBank. The CDS was cloned by RT-PCR and double digested to generate the expression vector pEGFP-N1-FOXO3. 4. Sequence analysis showed that the full-length FOXO3 CDS is 1467 bp, encoding 488 amino acids and is highly conserved across many bird species. Amino acid sequence analysis revealed a DNA-binding domain (aa 1-77). 5. Myoblast transfection with pEGFP-N1-FOXO3 showed that FOXO3 mRNA expression at 24 h was elevated in pEGFP-N1-FOXO3-transfected myoblasts compared to pEGFP-N1-transfected cells or controls. MRF4, MyoD, MyoG, Myf5 and PAX7 mRNA expression in the pEGFP-N1-FOXO3 group was lowest. However, myostatin (MSTN) and PAX3 mRNA expression did not differ. 6. These results suggest that FOXO3 plays a critical role in the proliferation and differentiation of duck myoblasts.

The cDNA sequence of the growth hormone receptor (GHR) from the black Muscovy duck was obtained and compared to the mRNA expression of growth hormone (GH) in the breast and leg muscles during 2-13 weeks of age using quantitative RT-PCR. The cDNA sequence of the Muscovy duck GHR gene is 1903 bp in length, with an 1830 bp coding region that encodes 609 amino acids. It exhibits > 92.9% homology with the poultry GHR cDNA and amino acid sequences. Overall, GHR mRNA expression was the highest at 2 weeks and the lowest at 13 weeks of age, exhibiting different profiles in different muscles. In the breast muscles, the GHR mRNA level declined sharply at 2-4 weeks, maintained at a plateau at 4-10 weeks and decreased slightly at 10-13 weeks. In the leg muscles, a gradual and slow decrease was observed during the whole period of 2-13 weeks. Robust extra-pituitary GH mRNA expression was detected in the muscles and the expression profile was highly correlated with that of GHR mRNA, in contrast to the inverse correlation between the pituitary GH and tissue GHR levels shown previously. These data suggest that the locally synthesised GH in the muscles, rather than the pituitary GH, is more closely associated with GHR and may be more critical for the regulation of muscle growth and contribute to the tissue-specific effects of GH.

Sudden death syndrome (SDS) in broilers is a cardiac disease associated with ventricular tachycardia (VT) and ventricular fibrillation (VF); however, its pathogenesis at the molecular level is not precisely determined. Downregulation and mutations of calsequestrin 2 (CASQ2), a major intracellular Ca(2+) buffer, have been associated with VT and sudden cardiac death (SCD) in humans but in chickens there is no report describing CASQ2 abnormalities in cardiac diseases. In order to better understand the molecular mechanisms predisposing the myocardium to fatal arrhythmia in broilers, the mRNA expression level of chicken CASQ2 gene (chCASQ2) in the left ventricle of dead broilers with SDS was determined and compared to healthy broilers using quantitative real-time PCR (qPCR). To determine the probable mutations in chCASQ2, PCR and direct sequencing were also done. Results showed a reduction in chCASQ2 expression in broilers dead by SDS. Three novel mutations (K289R, P308S, D310H) which are absent in healthy broilers were observed in chCASQ2. It is concluded that susceptibility to fatal cardiac arrhythmia in SDS may be associated with changes in intracellular Ca(2+) balance due to mutation and downregulation of chCASQ2.

1. cDNA sequence of gonadotropin-releasing-hormone receptor (GnRHR) gene was cloned and an association analysis between mutations and laying performance was conducted. 2. A 1680-bp cDNA sequence of Muscovy duck GnRHR, which encodes 415 amino acids, was obtained and characterised. Phylogenetic analysis revealed that Muscovy duck GnRHR has a close relationship with Gallus gallus GnRHR. 3. There were significantly different expression profiles between 4 age periods in the hypothalamus, pituitary, and ovary. The expression of GnRHR at the age of 36 weeks (laying period) was higher than other time points in the three tissues. GnRHR was expressed in 12 different tissues. The highest expression levels were observed in hypothalamus, pituitary and gonads. 4. A single nucleotide polymorphism detected in the second intron was associated with egg-laying performance. Individuals with genotype TT had better egg-laying performance from individuals with genotypes CC or TC. Therefore, GnRHR could be used as a marker gene for laying performance in Muscovy duck.

The objective of this investigation was to clone goose FSHβ-subunit cDNA and to construct a FSH fusion gene to identify the function of FSHβ mRNA during stages of the breeding cycle. The FSHβ gene was obtained by reverse transcription-PCR, and the full-length FSHβ mRNA sequence was amplified by rapid-amplification of cDNA ends. FSHβ mRNA expression was detected in reproductive tissues at different stages (pre-laying, laying period, and broody period). Additionally, the expression of 4 genes known to be involved in reproduction (FSHβ, GnRH, GH, and BMP) were evaluated in COS-7 cells expressing the fusion gene (pVITRO2-FSHαβ-CTP). The results show that the FSHβ gene consists of a 16 base pair (bp) 5'-untranslated region (UTR), 396 bp open reading frame, and alternative 3'-UTRs at 518 bp and 780 bp, respectively. qPCR analyses revealed that FSHβ mRNA is highly transcribed in reproductive tissues, including the pituitary, hypothalamus, ovaries, and oviduct. FSHβ mRNA expression increased and subsequently decreased in the pituitary, ovaries, and oviduct during the reproductive stages. Stable FSH expression was confirmed using enzyme-linked immunosorbent assays after transfection with the pVITRO2-FSHαβ-CTP plasmid. FSHβ, GnRH, and BMP expression increased significantly 36 h and 48 h after transfection with the fusion gene in COS-7 cells. The results demonstrate that the FSHβ subunit functions in the goose reproductive cycle and provides a theoretical basis for future breeding work.

Gonadotropin-releasing hormone (GnRH), a neuropeptide, plays a vital role in the hypothalamus-pituitary-gonadal (HPG) axis. In vertebrates, GnRH is crucial for the onset of sexual development and the entire reproductive process. The purpose of this study was to identify genetic factors associated with egg-laying traits of Muscovy ducks. The full-length cDNA (474 bp) of Muscovy duck GnRH was obtained and characterised. It encodes 92 amino acids containing a 1-amino acid signal peptide cleavage site. Phylogenetic analysis revealed that Muscovy duck GnRH has a close relationship with Anas platyrhynchos GnRH. GnRH showed significantly different expression profiles between 4 developmental periods in the hypothalamus, pituitary, and ovary. The expression of GnRH in the laying period (36 weeks) was higher than at other periods in the three tissues. GnRH was widely expressed in 12 examined tissues of nesting and laying Muscovy ducks. In the hypothalamus, pituitary and gonads, the expression of GnRH was higher than in other tissues. In laying Muscovy ducks, the expression of GnRH in the hypothalamus, pituitary, ovary, muscular stomach, pancreas, heart, duodenum and spleen was significantly higher than in nesting dusks. Differences were detected in the liver and glandular stomach between laying ducks and nesting ducks. Differences between the kidney and lung were not significant. In the pituitary, the GnRH and GnRH receptor (GnRHR) genes shared the same expression profiles during 4 time points. Both genes had the highest expression at 36 weeks of age. A mutation (g.206G > A) in the 5'-flanking region was associated with egg-laying performance. Individuals with genotype GG had better egg-laying performance than the individuals with genotype AA. GnRH may be used as a marker gene for laying performance in the Muscovy duck.

Introduction: Bone marrow transplantation is a critical approach for the treatment of many hematological disorders. Success of this approach is dependent on many factors the most important of which is the number of hematopoietic stem cells along with an efficient stroma. Co-transplantation of efficient mesenchymal stem cells can greatly improve the outcome of transplantations. Current researches assign a critical role for hypoxia inducible factor (HIF)-1α in protection of various cells and tissues probably through induction of cytokines. To make this feature applicable to human bone marrow-derived mesenchymal stem cells, we manipulated these cells to over express HIF-1α gene., Materials and Methods: Full-length cDNA of human HIF-1α was inserted into human bone marrow mesenchymal stem cells by pcDNA.3.1 non-viral plasmid vector, and the effect of this over expression on production of some hematopoietic growth factors was explored. Moreover, using a co-culture system, the interactive impact of HIF-1α-overexpressed mesenchymal stem cells on hematopoietic stem cells was evaluated. Results Over expression of HIF-1α in mesenchymal stem cells in normoxia increased production of one of the most important hematopoietic growth factors, Stem cell factor (also known as Steel factor or c-kit ligand). HIF-1α overexpression had no effect on production of other hematopoietic growth factors. In co-culture of mesenchymal stem cells-HIF-1α with hematopoietic stem cells, enhancement of colony formation and reduced differentiation of hematopoietic stem cells were observed. Conclusion Over expression of HIF-1α in human bone marrow-derived mesenchymal stem cells can augment the production of some hematopoietic growth factors, and we suggest this response of mesenchymal stem cells could help to improve the outcome of bone marrow transplantation.

We recently reported that hairpin (or stem-loop) priming is better-suited than polyA tailing to generate cDNA for plant microRNA qPCR. One major limitation of this method is the need to perform individual cDNA synthesis reactions for the reference gene and test miRNAs. Here, we report a novel fusion primer that allows multiplexed hairpin cDNA synthesis of the most-commonly used reference gene, nucleolar small RNA U6, together with test miRNAs. We also propose the use of miR1515 as a house keeping control for tropical legumes. We show that multiplexed cDNA synthesis does not result in loss of sensitivity and reduces the amount of RNA required for miRNA gene expression assays.

Macroautophagy (autophagy herein) is a cellular catabolic mechanism activated in response to stress conditions including starvation, hypoxia and misfolded protein accumulation. Abnormalities in autophagy were associated with pathologies including cancer and neurodegenerative diseases. Hence, elucidation of the signaling pathways controlling autophagy is of utmost importance. Recently we and others described microRNAs (miRNAs) as novel and potent modulators of the autophagic activity. Here, we describe MIR181A (hsa-miR-181a-1) as a new autophagy-regulating miRNA. We showed that overexpression of MIR181A resulted in the attenuation of starvation- and rapamycin-induced autophagy in MCF-7, Huh-7 and K562 cells. Moreover, antagomir-mediated inactivation of endogenous miRNA activity stimulated autophagy. We identified ATG5 as an MIR181A target. Indeed, ATG5 cellular levels were decreased in cells upon MIR181A overexpression and increased following the introduction of antagomirs. More importantly, overexpression of ATG5 from a miRNA-insensitive cDNA construct rescued autophagic activity in the presence of MIR181A. We also showed that the ATG5 3' UTR contained functional MIR181A responsive sequences sensitive to point mutations. Therefore, MIR181A is a novel and important regulator of autophagy and ATG5 is a rate-limiting miRNA target in this effect.

Adenosine to inosine deamination of RNA is widespread in metazoa. Inosines are recognized as guanosines and, therefore, this RNA-editing can influence the coding potential, localization and stability of RNAs. Therefore, RNA editing contributes to the diversification of the transcriptome in a flexible manner. The editing reaction is performed by adenosine deaminases that act on RNA (ADARs), which are essential for normal life and development in many organisms. Changes in editing levels are observed during development but also in neurological pathologies like schizophrenia, depression or tumors. Frequently, changes in editing levels are not reflected by changes in ADAR levels suggesting a regulation of enzyme activity. Until now, only a few factors are known that influence the activity of ADARs. Here we present a two-stage in vivo editing screen aimed to isolate enhancers of editing. A primary, high-throughput yeast-screen is combined with a more accurate secondary screen in mammalian cells that uses a fluorescent read-out to detect minor differences in RNA-editing. The screen was successfully employed to identify DSS1/SHFM1, the RNA binding protein hnRNP A2/B1 and a 3' UTR as enhancers of editing. By varying intracellular DSS1/SHFM1 levels, we can modulate A to I editing by up to 30%. Proteomic analysis indicates an interaction of DSS1/SHFM1 and hnRNP A2/B1 suggesting that both factors may act by altering the cellular RNP landscape. An extension of this screen to cDNAs from different tissues or developmental stages may prove useful for the identification of additional enhancers of RNA-editing.

We studied the effects of Zn(2+) on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn(2+) inactivated the activity of PSCK (IC(50) = .079 ± .004 mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn(2+) induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn(2+) directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn(2+) bind to PSCK and one Zn(2+) is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn(2+) with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn(2+) on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.

The NIa protease of Potyviridae is the major viral protease that processes potyviral polyproteins. The NIa protease coding region of Cardamom mosaic virus (CdMV) is amplified from the viral cDNA, cloned and expressed in Escherichia coli. NIa protease forms inclusion bodies in E.coli. The inclusion bodies are solubilized with 8 M urea, refolded and purified by Nickel-Nitrilotriacetic acid affinity chromatography. Three-dimensional modeling of the CdMV NIa protease is achieved by threading approach using the homologous X-ray crystallographic structure of Tobacco etch mosaic virus NIa protease. The model gave an insight in to the substrate specificities of the NIa proteases and predicted the complementation of nearby residues in the catalytic triad (H42, D74 and C141) mutants in the cis protease activity of CdMV NIa protease.

The calcineurin A (CaNA) subunit was identified as a novel binding partner of plasma membrane Na(+)/H(+) exchanger 1 (NHE1). CaN is a Ca(2+)-dependent phosphatase involved in many cellular functions, including cardiac hypertrophy. Direct binding of CaN to the (715)PVITID(720) sequence of NHE1, which resembles the consensus CaN-binding motif (PXIXIT), was observed. Overexpression of NHE1 promoted serum-induced CaN/nuclear factor of activated T cells (NFAT) signaling in fibroblasts, as indicated by enhancement of NFAT promoter activity and nuclear translocation, which was attenuated by NHE1 inhibitor. In neonatal rat cardiomyocytes, NHE1 stimulated hypertrophic gene expression and the NFAT pathway, which were inhibited by a CaN inhibitor, FK506. Importantly, CaN activity was strongly enhanced with increasing pH, so NHE1 may promote CaN/NFAT signaling via increased intracellular pH. Indeed, Na(+)/H(+) exchange activity was required for NHE1-dependent NFAT signaling. Moreover, interaction of CaN with NHE1 and clustering of NHE1 to lipid rafts were also required for this response. Based on these results, we propose that NHE1 activity may generate a localized membrane microdomain with higher pH, thereby sensitizing CaN to activation and promoting NFAT signaling. In cardiomyocytes, such signaling can be a pathway of NHE1-dependent hypertrophy.

1. A study was carried out to evaluate the expression of growth hormone (GH), insulin-like growth factor I (IGF-I), mitochondrial adenine nucleotide translocase (ANT), cytochrome oxidase III (COX III) and avian uncoupling protein (avUCP) genes in 14-d-old Japanese quail that were fed different levels of glycerol (0%, 4%, and 12% dietary glycerol) which replaced maize as an energy source. 2. Total RNA was extracted from the breast muscle, and cDNA was amplified using real-time PCR with primers specific to the examined genes. 3. Quail fed the diet with 12% glycerol supplementation presented higher growth hormone (GH) mRNA expression than did those fed 0% glycerol. Supplementation with 12% glycerol negatively influenced IGF-I mRNA expression and reduced ANT mRNA expression in comparison with the treatment with no glycerol. COX III mRNA expression in the pectoralis superficialis muscle was decreased by 26% in quail fed 12% glycerol compared with those fed 0 and 4% glycerol. 4. There was no difference in UCP mRNA expression between quail fed 0 and 4% glycerol; however, UCP expression was reduced (73%) in birds fed the 12% glycerol diet compared with the level in those fed the 4% glycerol diet. 5. The inclusion of 4% glycerol in the diet produced results similar to those of the diet with no glycerol. Based on quail performance and the expression of the GH, IGF-I, ANT, COX III and UCP genes, 4% glycerol can be used in quail feeding without any harmful effects.

Aptamers represent an emerging strategy to deliver cargo molecules, including dyes, drugs, proteins or even genes, into specific target cells. Upon binding to specific cell surface receptors aptamers can be internalized, for example by macropinocytosis or receptor mediated endocytosis. Here we report the in vitro selection and characterization of RNA aptamers with high affinity (Kd = 20 nM) and specificity for the human IL-6 receptor (IL-6R). Importantly, these aptamers trigger uptake without compromising the interaction of IL-6R with its natural ligands the cytokine IL-6 and glycoprotein 130 (gp130). We further optimized the aptamers to obtain a shortened, only 19-nt RNA oligonucleotide retaining all necessary characteristics for high affinity and selective recognition of IL-6R on cell surfaces. Upon incubation with IL-6R presenting cells this aptamer was rapidly internalized. Importantly, we could use our aptamer, to deliver bulky cargos, exemplified by fluorescently labeled streptavidin, into IL-6R presenting cells, thereby setting the stage for an aptamer-mediated escort of drug molecules to diseased cell populations or tissues.

1. Interleukin-6 (IL-6) is a multifunctional cytokine involved in lipid metabolism in adipose tissue. The objective of the study was to identify and characterize the IL-6 gene in the goose. 2. A full-length coding sequence (CDS) of the goose (Anser anser) IL-6 gene was cloned that encoded a 234-amino acid peptide containing a 38-amino acid signal peptide, an IL-6/G-CSF/MGF family consensus pattern and four conserved α-helices. The mature goose IL-6 showed 74% and 39% identities to that of chicken and human, respectively. 3. Quantitative real-time PCR analysis showed that the goose IL-6 was predominantly expressed in liver and was up-regulated in adipocytes by lipopolysaccharide (LPS) and oleic acid.

Mitophagy, the selective removal of mitochondria through the autophagic pathway, is involved in cellular mitochondria quality control. Dysfunctional mitochondria can be selectively eliminated through Parkin-mediated mitophagy. Parkin is a ubiquitin E3 ligase that selectively translocates onto impaired mitochondria to initiate mitophagy, and mutations in Parkin have been identified in autosomal recessive forms of Parkinson disease. Here with the use of a genetically encoded, mitochondria-matrix targeting photosensitizer, we established a robust strategy that allows for spatiotemporally controlled initiation of Parkin-mediated mitophagy in single cells with light. The method can specifically target varying numbers of mitochondria into the Parkin-mediated mitophagy pathway for clearance. Combined with live cell imaging, we demonstrated that mitochondria can be cleared by Parkin-mediated mitophagy without juxtanuclear mito-aggresome formation. Autophagy proceeded with the asynchronous appearance of small LC3B-coated structures on Parkin-labeled mitochondria subsections in a nucleation-expansion manner. Our method allows for quantitative measurement on the Parkin-mediated mitophagy process, and can be multiplexed in imaging for higher throughput studies.

It has been reported that the local introduction of a promoter-less DNA containing the complementary DNA (cDNA) sequence of a gene could induce gene-specific silencing in plants. The feasibility of this kind of silencing in human cancer cells is as yet unknown. The current study was designed to investigate the anti-tumor effects of a homologous promoterless K-ras cDNA system on pancreatic cancer. A full-length K-ras cDNA fragment was cloned into the promoterless plasmid puc19 to yield puc-K-ras. This construct was then transfected into pancreatic cancer cells. Our results demonstrated that the transfection of a promoterless K-ras cDNA resulted in a significant decrease in endogenous K-ras in a dose- and time-dependent manner and induced pancreatic cell apoptosis. Furthermore, stable puc-K-ras transfection decreased the endogenous protein level of K-ras and inhibited cell proliferation, clone formation and tumorigenicity in vivo. These findings indicate a promising application of this homologous promoterless cDNA silencing system in pancreatic cancer gene therapy.

Neogenin is a multifunctional receptor implicated in axon navigation, neuronal differentiation, morphogenesis, and cell death. Very little is known about signaling downstream of neogenin. Because we found that the neogenin intracellular domain (NeICD) interacts with nuclear proteins implicated in transcription regulation, we investigated further whether neogenin signals similarly to the Notch receptor. We show here that neogenin is cleaved by gamma-secretase, an event that releases the complete NeICD. We also describe that NeICD is located at the nucleus, a feature regulated through a balance between nuclear import and export. NeICD triggers gene reporter transactivation and associates with nuclear chromatin. Direct transcriptional targets of NeICD were determined and were shown to be up-regulated in the presence of neogenin ligand. Together, we reveal here a novel aspect of neogenin signaling that relies on the direct implication of its intracellular domain in transcriptional regulation.

DNA methylation-mediated transcriptional regulation is essential for human development and diverse diseases ensue when this process is dysregulated. Viruses, including HIV-1, alter the expression of human DNA methyltransferases (DNMTs) and various T cell-specific genes. Here we show that HIV-1 induction of DNMT1 results from overexpression of the early expressed HIV-1 proteins, and this induction is prevented with resveratrol which interferes with the transcription factor AP1 pathway. The HIV-1 responsive element resides in the 5' most 420 bp of the -1634 to +71 DNMT1 promoter; positioning of this truncated promoter proximal to a hybrid SV40-DNMT1 reporter results in HIV-1-dependent regulation. HIV-1 mediated induction of DNMT1 is not specific to T-cells, and does not require receptor-mediated endocytosis. The characterization of HIV-1 mediated DNMT1 regulation provides a basis for identifying viral and cellular factors necessary for the de novo DNA methylation of cellular genes.

The mobility of the Ty1 retrotransposon in the yeast Saccharomyces cerevisiae is restricted by a large collection of proteins that preserve the integrity of the genome during replication. Several of these repressors of Ty1 transposition (Rtt)/genome caretakers are orthologs of mammalian retroviral restriction factors. In rtt/genome caretaker mutants, levels of Ty1 cDNA and mobility are increased; however, the mechanisms underlying Ty1 hypermobility in most rtt mutants are poorly characterized. Here, we show that either or both of two S-phase checkpoint pathways, the replication stress pathway and the DNA damage pathway, partially or strongly stimulate Ty1 mobility in 19 rtt/genome caretaker mutants. In contrast, neither checkpoint pathway is required for Ty1 hypermobility in two rtt mutants that are competent for genome maintenance. In rtt101delta mutants, hypermobility is stimulated through the DNA damage pathway components Rad9, Rad24, Mec1, Rad53, and Dun1 but not Chk1. We provide evidence that Ty1 cDNA is not the direct target of the DNA damage pathway in rtt101delta mutants; instead, levels of Ty1 integrase and reverse transcriptase proteins, as well as reverse transcriptase activity, are significantly elevated. We propose that DNA lesions created in the absence of Rtt/genome caretakers trigger S-phase checkpoint pathways to stimulate Ty1 reverse transcriptase activity.

In organisms with sex chromosomes, dosage compensation equalizes gene expression between the sexes. In Drosophila melanogaster males, the male-specific lethal (MSL) complex of proteins and two noncoding roX RNAs coat the X chromosome, resulting in a twofold transcriptional upregulation to equalize gene expression with that of females. How MSL complex enrichment on the X chromosome is regulated is not well understood. We performed an RNA interference screen to identify new factors required for dosage compensation. Using a Drosophila Schneider S2 cell line in which green fluorescent protein (GFP)-tagged MSL2 localizes to the X chromosome, we assayed approximately 7,200 knockdowns for their effects on GFP-MSL2 distribution. One factor identified is the zinc finger protein Zn72D. In its absence, the MSL complex no longer coats the X chromosome. We demonstrate that Zn72D is required for productive splicing of the transcript for the MSL protein Maleless, explaining the dosage compensation defect. However, Zn72D is required for the viability of both sexes, indicating its functions are not sex specific. Consistent with this, Zn72D colocalizes with elongating RNA polymerase II, implicating it as a more general factor involved in RNA metabolism.

HM-30181, 4-oxo-4H-chromene-2-carboxylic acid [2-(2-{4-[2-(6,7-dimethoxy-3,4-dihydro-1H-isoquinolin-2-yl)-ethyl]-phenyl}-2H-tetrazol-5-yl)-4,5-dimethoxy-phenyl]-amide, is a new P-glycoprotein inhibitor with the potential to increase the cytotoxic activity of orally coadministered paclitaxel. This study was performed to characterize human cytochrome P-450 (CYP) enzymes involved in the metabolism of HM-30181 to 4- or 5-O-desmethyl-HM-30181 (M2) and 6- or 7-O-desmethyl-HM-30181 (M3) and to investigate the inhibitory potential of HM-30181 on CYP enzymes in human liver microsomes. CYP3A4 was identified as the major isozyme responsible for the O-demethylation of HM-30181 to M2 and M3 based on the correlation analysis, chemical inhibition and immuno-inhibition study and metabolism in cDNA-expressed human CYP isozymes. HM-30181 itself had no inhibitory effects on CYPs 1A2, 2A6, 2C8, 2C9, 2C19, 2D6, and 3A4 in human liver microsomes, suggesting the possibility that the pharmacokinetics of HM-30181 could be changed with coadministration of known CYP3A4 inducers or inhibitors.

Enzyme inhibition by fullerene derivatives has attracted much attention. In this communication, effects of two water-solube fullerene derivatives, fullerol and trimalonic acid C60 (TMA C60) on polymerase chain reaction (PCR) were investigated by using PCR of beta-actin cDNA derived from HeLa cells as an experimental model. Both fullerol and TMA C60 were found to inhibit PCR in a dose-dependent manner. PCR was ultimately inhibited while the concentrations of each compound were not less than 0.01 mM. In contrast, mannitol exerted no effects on PCR while its concentration increased up to 2 mM. Compensation experiments with Thermus aquaticus (Taq) DNA polymerase revealed that both fullerol and TMA C60 inhibited the enzymatic activity of Taq DNA polymerase, and the inhibitory potency of TMA C60 was slightly greater than that of fullerol. Our data provides some novel aspects on the enzyme inhibiting activities of fullerene derivatives.

Conclusion: The results show that alpha1D, alpha1E, alpha2/delta, beta1, and beta3 subunits are expressed in spiral ganglion cells (SGCs), and the coexpression of alpha1D and alpha1E suggests the presence of L-type and R-type calcium channels in mammalian SGCs., Objective: To investigate the types of subunits of voltage-gated calcium channels in SGCs of the mouse., Materials and Methods: SGCs were isolated from cochleae of neonatal mice and cultured for 24 h. Total RNA was extracted from cultured cells. After reverse transcription, the resulting cDNA was amplified by PCR with primers targeted to nucleotide sequences corresponding to seven different calcium channel subunits. The types of calcium channel subunits were identified by PCR analysis and nucleotide sequencing., Results: RT-PCR showed the strong and consistent amplification of alpha1D, alpha1E, alpha2/delta, beta1, and beta3 subunits from the mRNA of SGCs, and nucleotide sequencing confirmed the identity of mouse cochlear subunit cDNAs.

The transcriptional coactivator p/CIP(SRC-3/AIB1/ACTR/RAC3) binds liganded nuclear hormone receptors and facilitates transcription by directly recruiting accessory factors such as acetyltransferase CBP/p300 and the coactivator arginine methyltransferase CARM1. In the present study, we have established that recombinant p/CIP (p300/CBP interacting protein) is robustly methylated by CARM1 in vitro but not by other protein arginine methyltransferase family members. Metabolic labeling of MCF-7 breast cancer cells with S-adenosyl-L-[methyl-(3)H]methionine and immunoblotting using dimethyl arginine-specific antibodies demonstrated that p/CIP is specifically methylated in intact cells. In addition, methylation of full-length p/CIP is not supported by extracts derived from CARM1(-/-) mouse embryo fibroblasts, indicating that CARM1 is required for p/CIP methylation. Using mass spectrometry, we have identified three CARM1-dependent methylation sites located in a glutamine-rich region within the carboxy terminus of p/CIP which are conserved among all steroid receptor coactivator proteins. These results were confirmed by in vitro methylation of p/CIP using carboxy-terminal truncation mutants and synthetic peptides as substrates for CARM1. Analysis of methylation site mutants revealed that arginine methylation causes an increase in full-length p/CIP turnover as a result of enhanced degradation. Additionally, methylation negatively impacts transcription via a second mechanism by impairing the ability of p/CIP to associate with CBP. Collectively, our data highlight coactivator methylation as an important regulatory mechanism in hormonal signaling.

Increasing the proportion of bone marrow cells expression human multidrug resistance (MDR) 1 gene to prevent or circumvent bone morrow toxicity from chemotherapy agent is a high priority of dose intensification protocols. In this study, we have used a BALB/c mouse tumor-bearing model to investigate the chemoprotection effect of MDR1 gene by transfecting retroviral vectors containing and expressing the MDR gene in vivo. Hematopoietic progenitor cells served as a target of MDR1 gene transfer by the mediation of retrovirus vector and engrafted into the BALB/c mice with 60Co-gamma ray exposure in advance. Doxorubicin (5, 10, and 20 mg/kg) suppressed tumor growth of the xenograft significantly in dose-dependence mode if supported by suitable peripheral WBC. WBCs count revealed that the mice that had received gene-transduced cells showed a significant increase in WBCs count compared with their gene-transduced-naive counterparts. The function and expression of MDR1 gene were detected by flow cytometry, RT-PCR and immunohistochemistry (IC) method. MDRl mRNA expression could be detected in BM. Spleens contained measurable amounts of MDRl mRNA. Tail vein blood and tumor tissue detected MDRl DNA but no MDRl mRNA expression. FACS analysis of infected BM cells obtained 6 weeks later showed high levels of P-gp function. Based on these results we conclude that cytostatic drug resistance gene therapy may provide some degree of chemoprotection so can increase the chemotherapy dose to kill tumor cells.

A duplicated 3'-truncated version of RanGAP was previously identified as Segregation distorter (Sd), the meiotic drive gene in Drosophila melanogaster. Here we report the cloning and characterization of the complete gene sequence for the RanGAP homolog from the mosquito Aedes aegypti. The 1995 bp cDNA sequence consists of a 113 bp 5' UTR and 130 bp 3' UTR, and encodes a 583 amino acid protein with high sequence identity with RanGAP homologues of several species. A 20,125 bp genomic DNA sequence contains the complete RanGAP gene, consisting of three exons and two introns. Intron 2 comprises 18,082 bp and contains multiple repetitive elements as well as putative coding regions. The RanGAP locus was mapped to the q-arm of chromosome 2. Because the meiotic drive gene (M(D)) in A. aegypti was previously shown to be tightly linked with the sex determining locus on chromosome 1, RanGAP is likely not the M(D) gene.

DNA helicases are known to play important roles in the maintenance of genome integrity including the replication of trinucleotide repeats in the cells. Here, we report the HFM1 gene, which encodes the putative human DNA helicase. The HFM1 gene comprises 39 exons mapping to human chromosome 1p22.2. The HFM1 cDNA encompasses 4931 nucleotides with a single open reading frame (ORF) of 1435 amino acid residues encoding a predicted 172 kDa protein (hHFM1). The deduced protein sequence shares similar domain and motif structures to those of Mer3, a DNA helicase of Saccharomyces cerevisiae; seven consecutive motifs conserved among the DEXH-box type of DNA/RNA helicases at the N-terminal and a single putative zinc finger motif at the C-terminal regions of the protein. Further, the HFM1 transcript is preferentially expressed in testis and ovary. Collectively, hHFM1 is the evolutionally conserved putative human DNA helicase, which may function as a modulator for genome integrity in germ-line tissues.

Based on the amino acid information of trypsin inhibitor of buckwheat (Fagopyrum Esculentum Moench), degenerated primers were designed and a full-length cDNA sequence named BTIomega1 (Buckwheat Trypsin Inhibitor) was amplified from the leaves RNA by using RT-PCR and rapid amplification of cDNA ends (RACE) methods. Sequence analysis shows that the 392 bp cDNA contained an open reading frame (ORF) of 216 bp, encoding 72 amino acids residues. The deduced amino acid sequence exhibits 96 and 93% homology with BWI-1 and BTI-2, a natural trypsin inhibitor from buckwheat seeds. Southern blotting suggested that three copies of BTIomega1 gene existed in the buckwheat genome. Moreover, a predicted secondary structure and 3D-structural model was constructed by homology modeling. To our knowledge, this is the first all-round report of the gene BTIomega1. The novel BTIomega1 gene has been submitted to the GeneBank under Accession No. DQ289792.

A great many platforms and versions of the microarray technology, with different characteristics and applications, have been developed. This review will describe some key issues in reliability and performance with the two most commonly used platforms for gene expression analysis, in situ-synthesized oligonucleotide microarrays or GeneChips and spotted microarrays. Some recent advances and new applications within the field will be mentioned briefly.

The increasing use of microarray expression profiling to study the molecular biology of cancer and the cellular physiology of difficult-to-isolate cell types has led to a need for methods that accurately and precisely amplify small quantities of RNA. The purpose of this review is to provide an overview of the existing methods for transcriptome amplification and to define the parameters for comparing different amplification methods. The authors propose a standardized protocol for the assessment and evaluation of amplification methods, focusing on a new whole-transcriptome amplification kit, which amplifies total RNA into cDNA fragments. Reproducibility and reliability of the method were analyzed and discussed using both quantitative real-time PCR and a high-density oligonucleotide microarray platform.

Coxsackievirus B3 (CVB3) a close relative of Poliovirus has been implicated as the primary cause of dilated cardiomyopathy in humans. The single-stranded, plus sense, viral genomic RNA is naturally uncapped and the translation of viral encoded protein is initiated from an 'internal ribosome entry site' (IRES) element at the 5' untranslated region (UTR). The 741 nucleotide 5'UTR is highly structured, with defined stem loops. Previously, we have reported results of probing the secondary structure of the 5'UTR RNA, and showed the existence of 11 putative stem loop (SL) structures, SL A-K. Further, using mutants, we showed the importance of an apical GAGA loop in SL-H, in IRES activity. In addition to significantly reducing CVB3 IRES activity the mutations in the 5'UTR drastically reduced interaction with La autoantigen, a critical trans acting factor. Here, we demonstrate that mutation of the GAGA loop to CAGU alters the structure around SL-H, and reduces the interaction of La protein with critical cis acting elements of the IRES RNA. Interestingly, mutation of the loop to GAAA also has similar effect, suggesting the GAGA sequence of the loop, is necessary for the function. Furthermore, using gene specific siRNA against La protein we have demonstrated La protein to be a bona fide trans acting factor for CVB3 IRES. However, upon partial knockdown of La protein, translation mediated by the mutant 5'UTRs are affected to a similar extent as the wild type, implicating the structural alteration as the reason for the effect of the mutations on IRES activity.

Ribosome display presents an innovative in vitro technology for the rapid isolation and evolution of high-affinity peptides or proteins. Displayed proteins are bound to and recovered from target molecules in multiple rounds of selection in order to enrich for specific binding proteins. No transformation step is necessary, which could lead to a loss of library diversity. A cycle of display and selection can be performed in one day, enabling the existing gene repertoire to be rapidly scanned. Proteins isolated from the panning rounds can be further modified through random or directed molecular evolution for affinity maturation, as well as selected for characteristics such as protein stability, folding and functional activity. Recently, the field of display technologies has become more prominent due to the generation of new scaffolds for ribosome display, isolation of high-affinity human antibodies by phage display, and their implementation in the discovery of novel protein-protein interactions. Applications for this technology extend into the broad field of antibody engineering, proteomics, and synthetic enzymes for diagnostics and therapeutics in cancer, autoimmune and infectious diseases, neurodegenerative diseases and inflammatory disorders. This review highlights the role of ribosome display in drug discovery, discusses advantages and disadvantages of the system, and attempts to predict the future impact of ribosome display technology on the development of novel engineered biopharmaceutical products for biological therapies.

Compelling evidence suggests that deoxycytidine kinase (dCK), a key enzyme in the salvage of deoxyribonucleosides and in the activation of clinically relevant nucleoside analogues, can be regulated by reversible phosphorylation. In this study, we show that dCK overexpressed in HEK-293T cells was labelled after incubation of the cells with [32P]orthophosphate. Tandem mass spectrometry allowed the identification of 4 in vivo phosphorylation sites, Thr3, Ser11, Ser15, and Ser74. These results provide the first evidence that dCK is constitutively multiphosphorylated in intact cells. In addition, site-directed mutagenesis demonstrated that phosphorylation of Ser74, the major in vivo phosphorylation site, is crucial for dCK activity.

beta-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and it catalyses the irreversible hydrolysis of N-carbamyl-ss-aminoisobutyric acid or N-carbamyl-ss-alanine to beta-aminoisobutyric acid or ss-alanine, ammonia, and CO2. Analysis of the beta-ureidopropionase gene (UPB1) of the first 4 patients presenting with a complete enzyme deficiency, revealed the presence of 2 splice-site mutations (IVS1-2A>G and IVS8-1G>A) and one missense mutation (A85E). RT-PCR analysis of the complete beta-ureidopropionase cDNA suggested that both splice-site mutations lead to a variety of alternative splice variants, with deletions of a single or several exons. The alanine at position 85 was not conserved in other eukaryotic beta-ureidopropionase protein sequences.

Several recent studies indicate that mammals and other organisms produce large numbers of RNA transcripts that do not correspond to known genes. It has been suggested that these transcripts do not encode proteins, but may instead function as RNAs. However, discrimination of coding and non-coding transcripts is not straightforward, and different laboratories have used different methods, whose ability to perform this discrimination is unclear. In this study, we examine ten bioinformatic methods that assess protein-coding potential and compare their ability and congruency in the discrimination of non-coding from coding sequences, based on four underlying principles: open reading frame size, sequence similarity to known proteins or protein domains, statistical models of protein-coding sequence, and synonymous versus non-synonymous substitution rates. Despite these different approaches, the methods show broad concordance, suggesting that coding and non-coding transcripts can, in general, be reliably discriminated, and that many of the recently discovered extra-genic transcripts are indeed non-coding. Comparison of the methods indicates reasons for unreliable predictions, and approaches to increase confidence further. Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts.