Sample records for rb gene structure

  1. Exploring the structural and functional effect of pRB by significant nsSNP in the coding region of RB1 gene causing retinoblastoma.

    Rajasekaran, R; Sethumadhavan, Rao


    In this study, we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with E2F-2. Out of 956 SNPs, we investigated 12 nsSNPs in coding region in which three of them (SNPids rs3092895, rs3092903 and rs3092905) are commonly found to be damaged by I-Mutant 2.0, SIFT and PolyPhen programs. With this effort, we modeled the mutant pRB proteins based on these deleterious nsSNPs. From a comparison of total energy, stabilizing residues and RMSD of these three mutant proteins with native pRB protein, we identified that the major mutation is from Glutamic acid to Glycine at the residue position of 746 of pRB. Further, we compared the binding efficiency of both native and mutant pRB (E746G) with E2F-2. We found that mutant pRB has less binding affinity with E2F-2 as compared to native type. This is due to sixteen hydrogen bonding and two salt bridges that exist between native type and E2F-2, whereas mutant type makes only thirteen hydrogen bonds and one salt bridge with E2F-2. Based on our investigation, we propose that the SNP with an id rs3092905 could be the most deleterious nsSNP in RB1 gene causing retinoblastoma.

  2. Exploring the structural and functional effect of pRB by significant nsSNP in the coding region of RB1 gene causing retinoblastoma

    Rajasekaran; R; Rao; Sethumadhavan


    In this study,we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with E2F-2.Out of 956 SNPs,we investigated 12 nsSNPs in coding region in which three of them (SNPids rs3092895,rs3092903 and rs3092905) are commonly found to be damaged by I-Mutant 2.0,SIFT and PolyPhen programs.With this effort,we modeled the mutant pRB proteins based on these deleterious nsSNPs.From a comparison of total energy,stabilizing residues and RMSD of these three mutant proteins with native pRB protein,we identified that the major mutation is from Glutamic acid to Glycine at the residue position of 746 of pRB.Further,we compared the binding efficiency of both native and mutant pRB (E746G) with E2F-2.We found that mutant pRB has less binding affinity with E2F-2 as compared to native type.This is due to sixteen hydrogen bonding and two salt bridges that exist between native type and E2F-2,whereas mutant type makes only thirteen hydrogen bonds and one salt bridge with E2F-2.Based on our investigation,we propose that the SNP with an id rs3092905 could be the most deleterious nsSNP in RB1 gene causing retinoblastoma.


    ZENG Ji-bin; SONG Yue; WANG Yi; SHI Yu-yuan


    @@ Genetic alternations, such as mutations caused inactivities of tumor suppressor gene, have been identified in a wide variety of tumors, including osteosarcoma. Osteosarcoma is the most frequent primary malignant bone tumor that occurs in the extremities of young adolescents in most cases. Because of the high frequent occurrence of this type of tumor in hereditary retinoblastoma patients, involvement of the Rb1 gene mutations was suspected in the development of osteosarcoma, and a few reports have shown alternations of the Rb1 gene in osteosarcoma. We studied Rb1 gene mutations in 9 osteosarcoma samples and one cell line (OS 732) to explore the types and mechanism of Rb1 gene mutations in osteosarcoma.

  4. Crystal structure of Rb-elpasolite Rb{sub 2}NaAlF{sub 6}

    Yakubovich, O. V., E-mail:; Kiryukhina, G. V.; Dimitrova, O. V. [Moscow State University, Faculty of Geology (Russian Federation)


    Single crystals of Rb{sub 2}NaAlF{sub 6}, the Rb analogue of the mineral elpasolite, are obtained in the NaF-Rb{sub 2}CO{sub 3}-Al{sub 2}O{sub 3}-Rb{sub 3}PO{sub 4}-H{sub 2}O system under hydrothermal conditions, and their structure is determined by X-ray diffraction (R = 0.0188): a = 8.3087(1) A, space group Fm3bar m, Z = 4, and {rho}{sub calcd} = 3.88 g/cm{sup 3}. The hypothesis that Rb elpasolite exists in nature in late associations of pegmatites enriched in rubidium is proposed.

  5. Improved RB-HARQ scheme based on structured LDPC codes

    WANG Wen-jun; LIN Yue-wei; YAN Yuan


    Reliability-based hybrid automatic repeat request (ARQ) (RB-HARQ) is a recently introduced approach to incremental-redundancy ARQ. In RB-HARQ scheme, the bits that are to be retransmitted are adaptively selected at the receiver based on the estimated bit reliability. It could result in significant performance gain but requires huge overhead in the feedback channel. In this study, an improved RB-HARQ scheme (IRB-HARQ) for structured low-density parity-check codes is proposed, which simplifies the comparison operations needed to search the bits to be retransmitted and outperforms the RB-HARQ scheme in consideration of the bit transmission power for the requesting messages on the feedback link. Simulation results show that the IRB-HARQ scheme is more efficient and practical than the RB-HARQ scheme.

  6. Cloning and Molecular Characterization of the Schistosoma mansoni Genes RbAp48 and Histone H4

    Patrícia P Souza


    Full Text Available The human nuclear protein RbAp48 is a member of the tryptophan/aspartate (WD repeat family, which binds to the retinoblastoma (Rb protein. It also corresponds to the smallest subunit of the chromatin assembly factor and is able to bind to the helix 1 of histone H4, taking it to the DNA in replication. A cDNA homologous to the human gene RbAp48 was isolated from a Schistosoma mansoni adult worm library and named SmRbAp48. The full length sequence of SmRbAp48 cDNA is 1036 bp long, encoding a protein of 308 amino acids. The transcript of SmRbAp48 was detected in egg, cercariae and schistosomulum stages. The protein shows 84% similarity with the human RbAp48, possessing four WD repeats on its C-terminus. A hypothetical tridimensional structure for the SmRbAp48 C-terminal domain was constructed by computational molecular modeling using the b-subunit of the G protein as a model. To further verify a possible interaction between SmRbAp48 and S. mansoni histone H4, the histone H4 gene was amplified from adult worm genomic DNA using degenerated primers. The gene fragment of SmH4 is 294 bp long, encoding a protein of 98 amino acids which is 100% identical to histone H4 from Drosophila melanogaster.

  7. Detection of Tumor Suppressor Gene and Oncogene in SO-Rb_(50) Human Retinoblastoma Cell Line


    Retinoblastoma (Rb) is the most common malignant'cancer of eye. So-Rb_(50) is the first Rb cell line established in China in 1988. It has passed to the 387th passage now. We collected cells of the 327th passage of SO-Rb_(50), purified its genomic DNA and detected it with Rb and c-myc cDNA probes respectively (normal human white blood cells DNA was the control). We found the Rb gene was deleted while c-myc gene was amplified three times. This provides a basis for further study of the regulation of tumor ...


    Li Jian; Jiang Lei; Xia Yongjing; Li Hongxia; Hu Yajun; Hu Shixue; Xu Hongji


    Objective:To study the role of the most extensively studied tumor suppressor gene, retinoblastoma (Rb) gene,on the growth of lung adenocarcinoma cell line GLC-82 and explore a gene therapy approach for lung adenocarcinoma. Methods: The recombinant Rb gene adenovirus vector was constructed, the control virus which carries LacZ gene was producted by the same method. Infection effects were detected by biochemical staining of β-gal and immunohistochemical analysis of Rb protein. The Rb cDNA of infected cells were determined by PCR. The cell growth rate and cell cycle were observed by cell-counting and flow cytometry. Results: The constructed recombinant adenovirus vector could infect effectively the cells with high level expression of Rb cDNA and Rb protein. The transfection of wild-type Rb gene could suppress GLC-82 cell proliferation and decrease the cellular DNA synthesis. Conclusions: These results showed the possibility of using recombinant Rb gene adenovirus vector in the gene therapy of cancer to inhibit the growth of cancer.

  9. Conditional Deletion of the Retinoblastoma (Rb) Gene in Ovarian Granulosa Cells Leads to Premature Ovarian Failure

    Andreu-Vieyra, Claudia; Chen, Ruihong; Matzuk, Martin M.


    The retinoblastoma protein (RB) regulates cell proliferation and survival by binding to the E2F family of transcription factors. Recent studies suggest that RB also regulates differentiation in a variety of cell types, including myocytes, neurons, adipocytes, and chondrocytes. Rb mutations have been found in ovarian cancer; however, the role of RB in normal and abnormal ovarian function remains unclear. To test the hypothesis that loss of Rb induces ovarian tumorigenesis, we generated an ovarian granulosa cell conditional knockout of Rb (Rb cKO) using the Cre/lox recombination system. Rb cKO females showed 100% survival and no ovarian tumor formation through 9 months of age, but they developed progressive infertility. Prepubertal Rb cKO females showed increased ovulation rates compared with controls, correlating with increased follicle recruitment, higher Fshr and Kitl mRNA levels, and lower anti-Müllerian hormone levels. In contrast, the ovulation rate of 6-wk-old females was similar to that of controls. Morphometric analysis of Rb cKO ovaries from 6-wk-old and older females showed increased follicular atresia and apoptosis. Rb cKO ovaries and preantral follicles had abnormal levels of known direct and indirect target genes of RB, including Rbl2/p130, E2f1, Ccne2, Myc, Fos, and Tgfb2. In addition, preantral follicles showed increased expression of the granulosa cell differentiation marker Inha, decreased levels of Foxl2 and Cyp19a1 aromatase, and abnormal expression of the nuclear receptors Nr5a1, Nr5a2, and Nr0b1. Taken together, our results suggest that RB is required for the temporal-specific pattern of expression of key genes involved in follicular development. PMID:18599617

  10. Local structure of solid Rb at megabar pressures

    De Panfilis, S. [Centre for Life Nano Science IIT@Sapienza, Istituto Italiano di Tecnologia, I-00161 Roma (Italy); Gorelli, F.; Santoro, M. [INO-CNR and LENS, I-50019 Sesto Fiorentino, Firenze (Italy); Ulivi, L. [ISC-CNR, I-50019 Sesto Fiorentino, Firenze (Italy); Gregoryanz, E. [School of Physics and Astronomy, Centre for Science Under Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Irifune, T.; Shinmei, T. [Geodynamics Research Center, Ehime University, Matsuyama 790-8577 (Japan); Kantor, I.; Mathon, O.; Pascarelli, S. [European Synchrotron Radiation Facility, F-38043 Grenoble (France)


    We have investigated the local and electronic structure of solid rubidium by means of x-ray absorption spectroscopy up to 101.0 GPa, thus doubling the maximum investigated experimental pressure. This study confirms the predicted stability of phase VI and was completed by the combination of two pivotal instrumental solutions. On one side, we made use of nanocrystalline diamond anvils, which, contrary to the more commonly used single crystal diamond anvils, do not generate sharp Bragg peaks (glitches) at specific energies that spoil the weak fine structure oscillations in the x-ray absorption cross section. Second, we exploited the performance of a state-of-the-art x-ray focussing device yielding a beam spot size of 5 × 5 μm{sup 2}, spatially stable over the entire energy scan. An advanced data analysis protocol was implemented to extract the pressure dependence of the structural parameters in phase VI of solid Rb from 51.2 GPa up to the highest pressure. A continuous reduction of the nearest neighbour distances was observed, reaching about 6% over the probed pressure range. We also discuss a phenomenological model based on the Einstein approximation to describe the pressure behaviour of the mean-square relative displacement. Within this simplified scheme, we estimate the Grüneisen parameter for this high pressure Rb phase to be in the 1.3–1.5 interval.

  11. Mutational screening of the RB1 gene in Italian patients with retinoblastoma reveals 11 novel mutations.

    Sampieri, Katia; Hadjistilianou, Theodora; Mari, Francesca; Speciale, Caterina; Mencarelli, Maria Antonietta; Cetta, Francesco; Manoukian, Siranoush; Peissel, Bernard; Giachino, Daniela; Pasini, Barbara; Acquaviva, Antonio; Caporossi, Aldo; Frezzotti, Renato; Renieri, Alessandra; Bruttini, Mirella


    Retinoblastoma (RB, OMIM#180200) is the most common intraocular tumour in infancy and early childhood. Constituent mutations in the RB1 gene predispose individuals to RB development. We performed a mutational screening of the RB1 gene in Italian patients affected by RB referred to the Medical Genetics of the University of Siena. In 35 unrelated patients, we identified germline RB1 mutations in 6 out of 9 familial cases (66%) and in 7 out of 26 with no family history of RB (27%). Using the single-strand conformational polymorphism (SSCP) technique, 11 novel mutations were detected, including 3 nonsense, 5 frameshift and 4 splice-site mutations. Only two of these mutations (1 splice site and 1 missense) were previously reported. The mutation spectrum reflects the published literature, encompassing predominately nonsense or frameshift and splicing mutations. RB1 germline mutation was detected in 37% of our cases. Gross rearrangements outside the investigated region, altered DNA methylation, or mutations in non-coding regions, may be the cause of disease in the remainder of the patients. Some cases, e.g. a case of incomplete penetrance, or variable expressivity ranging from retinoma to multiple tumours, are discussed in detail. In addition, a case of pre-conception genetic counselling resolved by rescue of banked cordonal blood of the affected deceased child is described.

  12. Experimental research of RB94 gene transfection into retinoblastoma cells using ultrasound-targeted microbubble destruction.

    Zheng, Min-Ming; Zhou, Xi-Yuan; Wang, Li-Ping; Wang, Zhi-Gang


    The purpose of this study was to explore the transfection of the recombinant expression plasmid pEGFP-C1/RB94 into human retinoblastoma cells (HXO-Rb44) using ultrasound-targeted microbubble destruction (UTMD). pEGFP-C1/RB94 was transfected into HXO-Rb44 in vitro by UTMD, with liposome as the positive control. After 24 to 72 h, the expression of the reporter gene enhanced green fluorescent protein (EGFP) was observed using fluorescent microscopy and flow cytometry. The cell viability of HXO-Rb44 was measured by a MTT assay. The mRNA and proteins of RB94, caspase-3 and Bax were analyzed by reverse transcription polymerase chain reaction (RT-PCR) and Western blot. Moreover, the apoptosis rate and cell cycle progression of the cells were detected by flow cytometry. This study demonstrated that UTMD can enhance the transfection efficiency of RB94, which has an obvious impact on the inhibition of the growth process of retinoblastoma cells, suggesting that the combination of UTMD and RB94 compounds might be a useful tool for use in the gene therapy of retinoblastoma.

  13. Cooperative activation of tissue-specific genes by pRB and E2F1.

    Flowers, Stephen; Xu, Fuhua; Moran, Elizabeth


    The retinoblastoma tumor suppressor protein pRB is conventionally regarded as an inhibitor of the E2F family of transcription factors. Conversely, pRB is also recognized as an activator of tissue-specific gene expression along various lineages including osteoblastogenesis. During osteoblast differentiation, pRB directly targets Alpl and Bglap, which encode the major markers of osteogenesis alkaline phosphatase and osteocalcin. Surprisingly, p130 and repressor E2Fs were recently found to cooccupy and repress Alpl and Bglap in proliferating osteoblast precursors before differentiation. This raises the further question of whether these genes convert to E2F activation targets when differentiation begins, which would constitute a remarkable situation wherein pRB and E2F would be cotargeting genes for activation. Chromatin immunoprecipitation analysis in an osteoblast differentiation model shows that Alpl and Bglap are indeed targeted by an activator E2F, i.e., is E2F1. Promoter occupation of Alpl and Bglap by E2F1 occurs specifically during activation, and depletion of E2F1 severely impairs their induction. Mechanistically, promoter occupation by E2F1 and pRB is mutually dependent, and without this cooperative effect, activation steps previously shown to be dependent on pRB, including recruitment of RNA polymerase II, are impaired. Myocyte- and adipocyte-specific genes are also cotargeted by E2F1 and pRB during differentiation along their respective lineages. The finding that pRB and E2F1 cooperate to activate expression of tissue-specific genes is a paradigm distinct from the classical concept of pRB as an inhibitor of E2F1, but is consistent with the observed roles of these proteins in physiological models.

  14. The tumor suppressor Rb and its related Rbl2 genes are regulated by Utx histone demethylase

    Terashima, Minoru; Ishimura, Akihiko; Yoshida, Masakazu [Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa (Japan); Suzuki, Yutaka; Sugano, Sumio [Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Chiba (Japan); Suzuki, Takeshi, E-mail: [Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa (Japan)


    Research highlights: {yields} Utx increases expression of Rb and Rbl2 genes through its demethylase activity. {yields} Utx changes histone H3 methylation on the Rb and Rbl2 promoters. {yields} Utx induces decreased cell proliferation of mammalian primary cells. -- Abstract: Utx is a candidate tumor suppressor gene that encodes histone H3 lysine 27 (H3K27) demethylase. In this study, we found that ectopic expression of Utx enhanced the expression of retinoblastoma tumor suppressor gene Rb and its related gene Rbl2. This activation was dependent on the demethylase activity of Utx, and was suggested to contribute to the decreased cell proliferation induced by Utx. A chromatin immunoprecipitation assay showed that over-expressed Utx was associated with the promoter regions of Rb and Rbl2 resulting in the removal of repressive H3K27 tri-methylation and the increase in active H3K4 tri-methylation. Furthermore, siRNA-mediated knockdown of Utx revealed the recruitment of endogenous Utx protein on the promoters of Rb and Rbl2 genes. These results indicate that Rb and Rbl2 are downstream target genes of Utx and may play important roles in Utx-mediated cell growth control.

  15. A comprehensive, sensitive and economical approach for the detection of mutations in the RB1 gene in retinoblastoma

    Vidya Latha Parsam; Chitra Kannabiran; Santosh Honavar; Geeta K. Vemuganti; Mohammad Javed Ali


    Retinoblastoma (Rb) is the most common primary intraocular malignancy in children. It is brought about by the mutational inactivation of both alleles of RB1 gene in the developing retina. To identify the RB1 mutations, we analysed 74 retinoblastoma patients by screening the exons and the promoter region of RB1. The strategy used was to detect large deletions/duplications by fluorescent quantitative multiplex PCR; small deletions/insertions by fluorescent genotyping of RB1 alleles, and point mutations by PCR-RFLP and sequencing. Genomic DNA from the peripheral blood leucocytes of 74 Rb patients (53 with bilateral Rb, 21 with unilateral Rb; 4 familial cases) was screened for mutations. Recurrent mutations were identified in five patients with bilateral Rb, large deletions in 11 patients (nine with bilateral Rb and two with unilateral Rb), small deletions/insertions were found in 12 patients all with bilateral Rb, and point mutations in 26 patients (14 nonsense, six splice site, five substitution and one silent change). Three mutations were associated with variable expressivity of the disease in different family members. Using this method, the detection rates achieved in patients with bilateral Rb were 44/53 (83%) and with unilateral Rb, 5/21 (23.8%). This approach may be feasible for clinical genetic testing and counselling of patients.

  16. Resistance to Phytophthora infestans EC-1 clonal lineage in Solanum tuberosum by introducing the RB gene

    María Lupe Román


    Full Text Available One of the most efficient options for the control of late blight disease in potato (Solanum tuberosum is the development of resistant varieties to Phytophthora infestans mediated by the direct transfer of resistance (R genes through genetic engineering. In the present work, we used Solanum bulbocastanum RB gene to confers broad spectrum resistance to P. infestans races. To that end, Agrobacterium - mediated genetic transformation was used to transform a susceptible potato variety, Desiree, with the binary vector pCIP68 harboring the RB gene. As a result, 19 transformed plants containing the RB gene were obtained. kanamycin resistance test and polymerase chain reaction (PCR assays confirmed the integration of the T-DNA in the potato genome. The 19 transformed plants, also called transgenic events were subjected to infection under biosafety greenhouse conditions. Phytophthora infestans isolate POX067 of the EC-1 clonal lineage, commonly find in Peru, was used for the infection. Three of the 19 plants ([RB]54, [RB]56 and [RB]70 show high resistance levels to isolate POX067 of P. infestans.

  17. Experimental Model to Study the Role of Retinoblastoma Gene Product (pRb) for Determination of Adipocyte Differentiation.

    Popov, B V; Shilo, P S; Zhidkova, O V; Zaichik, A M; Petrov, N S


    Using stable constitutive expression of retinoblastoma gene product (pRb) in polypotent mesenchymal 10T1/2 cells we obtained stable cell lines hyperexpressing functionally active or inactive mutant pRb. The cells producing active exogenous pRb demonstrated high sensitivity to adipocyte differentiation inductors, whereas production of inactive form of the exogenous protein suppressed adipocyte differentiation. The obtained lines can serve as the experimental model for studying the role of pRb in determination of adipocyte differentiation.

  18. 视肉膜母细胞瘤(RB)抑癌基因治疗原理及策略%Principles and Strategies for Approaching Retinoblastoma (RB) Tumor Suppressor Gene Therapy

    徐洪基; 缪庆; 胡诗学; 刘秉慈


    The retinoblastoma (RB) gene was the first tumor suppressor gene identified.It encodes a nuclear phosphoprotein which is differentially phosphorylated during the cell cycle.And the RB gene apparently plays a key role in cell growth regulation.Mutations in RB are seen in virtually all cases of retinoblastoma,and loss of RB gene function has been implicated in the progression of many common human cancers.A number of studies have indicated that replacement of the normal RB gene in RB-defective tumor cells could suppress their tumorigenic activity in nude mice.Preclinical studies also demonstrated that treatment of established human xenograft tumors in nude mice by recombinant adenovirus vectors expressing RB protein resulted in regression of the treated tumor.These studies make the emerging RB gene therapy even more attraction.

  19. pRB is required for interferon-gamma-induction of the MHC class II abeta gene.

    Zhu, X; Pattenden, S; Bremner, R


    pRB is required for IFN-gamma-induction of MHC class II in human tumor cell lines, providing a potential link between tumor suppressors and the immune system. However, other genes, such as cyclin D1, show pRB-dependency only in tumor cells, so by analogy, pRB may not be necessary for cII-regulation in normal cells. Here, we demonstrate that induction of the mouse MHC class II I-A heterodimer is normal in RB+/+ mouse embryonic fibroblasts (MEFs), but deficient in RB-/- MEFs. Inducibility is restored in RB-/- MEFs stably transfected with wild type RB cDNA or infected with an adenovirus expressing pRB. Thus, involvement of pRB in MHC class II expression is conserved in the mouse and is not an aberrant feature of tumorigenic, aneuploid, human tumor cells. Although cII genes are generally induced in a coordinate fashion, suggesting a common mechanism, we found that pRB was specifically required for induction of the Abeta, but not Aalpha or other MHC cII genes including Ebeta, Ii and H2-Malpha. Finally, IFN-gamma-induction of class II transactivator (CIITA), was pRB-independent, suggesting that pRB works downstream of this master-regulator of MHC class II expression.

  20. Rb and p53 gene deletions in lung adenocarcinomas from irradiated and control mice

    Zhang, Y.; Woloschak, G.E. [Argonne National Lab., IL (United States). Center for Mechanistic Biology and Biotechnology


    This study was conducted on mouse lung adenocarcinoma tissues that were formalin-treated and paraffin-embedded 25 years ago to investigate the large gene deletions of mRb and p53 in B6CF{sub 1} male mice. A total of 80 lung tissue samples from irradiated mice and 40 lung samples from nonirradiated controls were randomly selected and examined in the mRb portion of this study. The results showed a significant (P < 0.05) higher percentage of mRb deletions in lung adenocarcinomas from mice exposed to 60 once-weekly {gamma}-ray doses than those from mice receiving 24 once-weekly {gamma}-ray doses at low doses and low dose rates; however, the percentage was not significantly different (P > 0.05) from that for spontaneous lung adenocarcinomas or lung adenocarcinomas from mice exposed to single-dose {gamma} irradiation at a similar total dose. mRb fragments 3 (71%) and 5 (67%), the parts of the gene that encoded the pocket binding region of Rb protein to adenovirus E1A and SV40 T-antigen, were the most frequently deleted fragments. p53 gene deletion analysis was carried out on normal lungs and lung adenocarcinomas that were initially found to bear mRb deletions. Exons 1,4,5,6, and 9 were chosen to be analyzed.

  1. 5-Aza-2'-deoxycytidine reactivates gene expression via degradation of pRb pocket proteins.

    Zheng, Zhixing; Li, Lian; Liu, Xiangyu; Wang, Donglai; Tu, Bo; Wang, Lina; Wang, Haiying; Zhu, Wei-Guo


    Not only does 5-aza-2'-deoxycytidine (5-aza-CdR) induce the reexpression of silenced genes through the demethylation of CpG islands, but it increases the expression of unmethylated genes. However, the mechanism by which 5-aza-CdR activates the expression of genes is not completely understood. Here, we report that the pRb pocket proteins pRb, p107, and p130 were degraded in various cancer cell lines in response to 5-aza-CdR treatment, and this effect was dependent on the proteasome pathway. Mouse double minute 2 (MDM2) played a critical role in this 5-aza-CdR-induced degradation of pRb. Furthermore, PP2A phosphatase-induced MDM2 dephosphorylation at S260 was found to be essential for MDM2 binding to pRb in the presence of 5-aza-CdR. pRb degradation resulted in the significant reexpression of several genes, including methylated CDKN2A, RASFF1A, and unmethylated CDKN2D. Finally, knockdown of pRb pocket proteins by either RNAi or 5-aza-CdR treatment induced a significant decrease in the recruitment of SUV39H1 and an increase in the enrichment of KDM3B and KDM4A to histones around the promoter of RASFF1A and thus reduced H3K9 di- and trimethylation, by which RASFF1A expression is activated. Our data reveal a novel mechanism by which 5-aza-CdR induces the expression of both methylated and unmethylated genes by degrading pRb pocket proteins.

  2. RB1 in cancer: different mechanisms of RB1 inactivation and alterations of pRb pathway in tumorigenesis.

    Di Fiore, Riccardo; D'Anneo, Antonella; Tesoriere, Giovanni; Vento, Renza


    Loss of RB1 gene is considered either a causal or an accelerating event in retinoblastoma. A variety of mechanisms inactivates RB1 gene, including intragenic mutations, loss of expression by methylation and chromosomal deletions, with effects which are species-and cell type-specific. RB1 deletion can even lead to aneuploidy thus greatly increasing cancer risk. The RB1gene is part of a larger gene family that includes RBL1 and RBL2, each of the three encoding structurally related proteins indicated as pRb, p107, and p130, respectively. The great interest in these genes and proteins springs from their ability to slow down neoplastic growth. pRb can associate with various proteins by which it can regulate a great number of cellular activities. In particular, its association with the E2F transcription factor family allows the control of the main pRb functions, while the loss of these interactions greatly enhances cancer development. As RB1 gene, also pRb can be functionally inactivated through disparate mechanisms which are often tissue specific and dependent on the scenario of the involved tumor suppressors and oncogenes. The critical role of the context is complicated by the different functions played by the RB proteins and the E2F family members. In this review, we want to emphasize the importance of the mechanisms of RB1/pRb inactivation in inducing cancer cell development. The review is divided in three chapters describing in succession the mechanisms of RB1 inactivation in cancer cells, the alterations of pRb pathway in tumorigenesis and the RB protein and E2F family in cancer.

  3. Molecular cloning, expression pattern analysis of porcine Rb1 gene and its regulatory roles during primary dedifferentiated fat cells adipogenic differentiation.

    Hu, Xiaoming; Luo, Pei; Peng, Xuewu; Song, Tongxing; Zhou, Yuanfei; Wei, Hongkui; Peng, Jian; Jiang, Siwen


    Adipocytes are the main constituent of adipose tissue and are considered to be a corner stone in the homeostatic control of whole body metabolism. Recent reports evidenced that retinoblastoma 1 (Rb1) gene plays an important role in fat development and adipogenesis in mice. Here, we cloned the partial cDNA sequences of the porcine Rb1 gene which contains the complete coding sequences (CDS) of 2820bp encoding a protein of 939 amino acids. Bioinformatic analysis revealed that the CDS of porcine Rb1 was highly identical with those of cattle, human and mice. The porcine Rb1 has three typical conserved structural domains, including Rb-A pocket domain, CYCLIN domain and C-terminus domain, and the phylogenetic tree indicates a closer genetic relationship with cattle and human. Tissue distribution analysis showed that Rb1 expression appeared to be ubiquitously in various tissues, being higher in heart, liver, muscle, and stomach. Furthermore, significant downregulation of Rb1 was found at the initial stage of dedifferentiated fat (DFAT) cells adipogenic differentiation. With the knockdown of the Rb1 expression by siRNA, the number of DFAT cells recruited to white rather than brown adipogenesis was promoted, and mRNA levels of adipogenic markers, such as PPARγ, aP2, LPL and adiponectin and protein expression of PPARγ and adiponectin were increased after hormone stimulation. The underlying mechanisms may be that knockdown of Rb1 promotes the mitotic clonal expansion and PPARγ expression by derepressing the transcriptional activity of E2F so as to facilitate the first steps of adipogenesis. In summary, we cloned and characterized an important negative regulator in adipogenic commitment of porcine DFAT cells.

  4. Mutational analysis of the RB1 gene and the inheritance patterns of retinoblastoma in Jordan.

    Yousef, Yacoub A; Tbakhi, Abdelghani; Al-Hussaini, Maysa; AlNawaiseh, Ibrahim; Saab, Ala; Afifi, Amal; Naji, Maysa; Mohammad, Mona; Deebajah, Rasha; Jaradat, Imad; Sultan, Iyad; Mehyar, Mustafa


    Retinoblastoma (RB) is a childhood cancer developing in the retina due to RB1 pathologic variant. Herein we are evaluating the oncogenic mutations in the RB1 gene and the inheritance patterns of RB in the Jordanian patients. In this prospective study, the peripheral blood of 50 retinoblastoma patients was collected, genomic DNA was extracted, mutations were identified using Quantitative multiplex PCR (QM-PCR), Allele-specific PCR, Next Generation Sequencing analysis, and Sanger sequencing. In this cohort of 50 patients, 20(40%) patients had unilateral RB and 30(60%) were males. Overall, 36(72%) patients had germline disease, 17(47%) of whom had the same RB1 pathologic variant detected in one of the parents (inherited disease). In the bilateral group, all (100%) patients had germline disease; 13(43%) of them had inherited mutation. In the unilateral group, 6(30%) had germline disease, 4(20%) of them had inherited mutation. Nonsense mutation generating a stop codon and producing a truncated non-functional protein was the most frequent detected type of mutations (n = 15/36, 42%). Only one (2%) of the patients had mosaic mutation, and of the 17 inherited cases, 16(94%) had an unaffected carrier parent. In conclusion, in addition to all bilateral RB patients in our cohort, 30% of unilateral cases showed germline mutation. Almost half (47%) of germline cases had inherited disease from affected (6%) parent or unaffected carrier (94%). Therefore molecular screening is critical for the genetic counseling regarding the risk for inherited RB in both unilateral and bilateral cases including those with no family history.

  5. Ultralong-Range Rb-KRb Rydberg Molecules: Selected Aspects of Electronic Structure, Orientation and Alignment

    Aguilera-Fernández, Javier; Sadeghpour, H. R.; Schmelcher, Peter; González-Férez, Rosario


    We investigate the structure and features of an ultralong-range triatomic Rydberg molecule formed by a Rb Rydberg atom and a KRb diatomic molecule. In our numerical description, we perform a realistic treatment of the internal rotational motion of the diatomic molecule, and take into account the Rb(n, l ≥ 3) Rydberg degenerate manifold and the energetically closest neighboring levels with principal quantum numbers n' > n and orbital quantum number l ≤ 2. We focus here on the adiabatic electronic potentials evolving from the Rb(n,l ≥ 3) and Rb(n = 26, l = 2) manifolds. The directional properties of the KRb diatomic molecule within the Rb-KRb triatomic Rydberg molecule are also analyzed in detail.

  6. Ultralong-Range Rb-KRb Rydberg Molecules: Selected Aspects of Electronic Structure, Orientation and Alignment

    Aguilera-Fernández, Javier; Schmelcher, Peter; González-Férez, Rosario


    We investigate the structure and features of an ultralong-range triatomic Rydberg molecule formed by a Rb Rydberg atom and a KRb diatomic molecule. In our numerical description, we perform a realistic treatment of the internal rotational motion of the diatomic molecule, and take into account the Rb($n, l\\ge 3$) Rydberg degenerate manifold and the energetically closest neighboring levels with principal quantum numbers $n'>n$ and orbital quantum number $l\\le2$. We focus here on the adiabatic electronic potentials evolving from the Rb($n, l\\ge 3$) and Rb($n=26, l=2$) manifolds. The directional properties of the KRb diatomic molecule within the Rb-KRb triatomic Rydberg molecule are also analyzed in detail.

  7. Expression of p16 gene and Rb protein in gastric carcinoma and their clinicopathological significance

    Xiu-Sheng He; Ying-Hui Rong; Qi Su; Qiao Luo; Dong-Mei He; Yan-Lan Li; Yan Chen


    AIM: To analyze the correlation between the protein expression of p16 and Rb genes in gastric carcinoma (GC),to investigate the role of p16 gene in invasion and lymph node metastasis of GC, and to examine the deletion and mutation in exon 2 of p16 gene in GC.METHODS: The protein expression of p16 and Rb genes was examined by streptavidin-peroxidase conjugated method (S-P) in normal gastric mucosa, dysplastic gastric mucosa and GC. The deletion and mutation of p16 gene were examined by polymerase chain reaction (PCR) and polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) respectively in normal gastric mucosa and GC.RESULTS: The positive rates of P16 and Rb protein expression respectively were 96% (77/80) and 99%(79/80) in normal gastric mucosa, 92% (45/50) and 80%(40/50) in dysplastic gastric mucosa, 48% (58/122) and 60% (73/122) in GC. The positive rates of P16 and Rb protein expression in GC were significantly lower than that in normal gastric mucosa and dysplastic gastric mucosa (P<0.05). The positive rate of P16 protein expression in mucoid carcinoma (10%, 1/10) was significantly lower than that in poorly differentiated carcinoma (51%, 21/41),undifferentiated carcinoma (58%, 15/26) and signet ring cell carcinoma (62%, 10/16) (P<0.05). The positive rates of P16 protein in 30 cases of paired primary and lymph node metastatic GC were 47% (14/30) and 17% (5/30)respectively, being significantly lower in the later than in the former (P<0.05). There was no mutation in exon 2 of p16 gene in the 25 freshly resected primary GCs. But five cases in the 25 freshly resected primary GCs displayed deletion in exon 2 of p16 gene. The positive rate of both P16 and Rb proteins was 16% (14/90), and the negative rate of both P16 and Rb proteins was 8% (7/90) in 90GCs. The rate of positive P16 protein with negative Rb protein was 33% (30/90). The rate of negative P16 protein with positive Rb protein was 43% (39/90). There was reverse correlation

  8. Preparation and Structural Characterization of Superionic Conductor RbAg4I5 Crystalline Grain Film

    曹阳; 孙红三; 孙家林; 田广彦; 邢志; 郭继华


    Superionic conductor RbAg4I5 crystalline grainfilms were prepared by vacuum thermal evaporation on NaCl crystalline substrates. The surface morphology, microstructure and the electronic energy states of the films were examined by atomic force microscopy, transmission-electron microscopy, x-ray diffraction and x-ray photoelectron spectroscopy. The results show that the obtained RbAg4I5 layer has an epitaxial film of perfect crystalline structure, and the unit cell of crystalline grain RbAg4I5 films belongs to cubic crystal system. The principal x-ray diffraction peaks at d = 3.7447 and 1.8733A are related to the structure of ternary compound RbAg4I5films.

  9. Preparation and Structural Characterization of Superionic Conductor RbAg4I5 Crystalline Grain Film

    Cao, Yang; Sun, Hong-San; Sun, Jia-Lin; Tian, Guang-Yan; Xing, Zhi; Guo, Ji-Hua


    Superionic conductor RbAg4I5 crystalline grain films were prepared by vacuum thermal evaporation on NaCl crystalline substrates. The surface morphology, microstructure and the electronic energy states of the films were examined by atomic force microscopy, transmission-electron microscopy, x-ray diffraction and x-ray photoelectron spectroscopy. The results show that the obtained RbAg4I5 layer has an epitaxial film of perfect crystalline structure, and the unit cell of crystalline grain RbAg4I5 films belongs to cubic crystal system. The principal x-ray diffraction peaks at d = 3.7447 and 1.8733 Å are related to the structure of ternary compound RbAg4I5 films.

  10. High expression of RbAp46 gene in patients with acute leukemia or chronic myelogenous leukemia in blast crisis

    HU Shao-yan; CHEN Zi-xing; GU Wei-ying; CEN Jian-nong; ZHAO Ye


    @@ The retinoblastoma (Rb) suppressor associated protein 46 (RbAp46) also named retinoblastoma binding protein 7 (RBBP7) was first identified as a protein in HeLa cells that binds to an Rb affinity column.RbAp46 has been shown to be a core component of the mSin3 histone deacetylase (HDAC) complex1 and NuRD ( a multi-subunit complex containing chromosome-remodeling activity).2 RbAp46 is also known as the histone acetyltransferase (HAT) type B subunit 2.3 Thus,RbAp46 functions as a core-histone-binding subunit that targets chromatin assembly factors,chromatin-remodeling factors,histone acetyltransferase and deacetylase to their histone substrates in chromatin.Guan et al4 isolated RbAp46 as a downstream target gene of the Wilms'tumor suppressor gene (WT1),mediating the function of WT1.It has been discovered recently that RbAp46 specifically interacts with the BRCT domain of breast cancer and ovarian cancer susceptibility gene BRCA1 and modulates its transcriptional transactivation activity.5

  11. Identification of target genes of the p16INK4A-pRB-E2F pathway

    Vernell, Richard; Helin, Kristian; Müller, Heiko


    Deregulation of the retinoblastoma protein (pRB) pathway is a hallmark of human cancer. The core members of this pathway include the tumor suppressor protein, pRB, which through binding to a number of cellular proteins, most notably members of the E2F transcription factor family, regulates...... progression through the cell division cycle. With the aim of identifying transcriptional changes provoked by deregulation of the pRB pathway, we have used cell lines that conditionally express a constitutively active phosphorylation site mutant of pRB (pRBDeltaCDK) or p16INK4A (p16). The expression of p...... as physiological targets of the pRB pathway, and the further characterization of these genes should provide insights into how this pathway controls proliferation. We show that Gibbs sampling detects enrichment of several sequence motifs, including E2F consensus binding sites, in the upstream regions of these genes...

  12. Direct estimation of the recombination frequency between the RB1 gene and two closely linked microsatellites using sperm typing.

    Girardet, A; Lien, S; Leeflang, E P; Beaufrère, L; Tuffery, S; Munier, F; Arnheim, N; Claustres, M; Pellestor, F


    In this study, single sperm typing has been used for high-resolution recombination analysis between the retinoblastoma gene and two closely linked extragenic microsatellites (D13S284 and D13S1307). The analysis of 1198 single sperm from three donors allowed the determination of recombination fractions between RB1.20 and D13S284 and RB1.20 and D13S1307 of 0.022 and 0.033, respectively. These results show that RB1 gene and the two microsatellites are closely linked, which validates their potential use in indirect genetic diagnosis of retinoblastoma.

  13. Study of polymorphisms in the TP53 and RB1 genes in children with retinoblastoma in northern Mexico

    Nares-Cisneros, Jesús; Cárdenas-Hernández, Rubén I.; Jaramillo-Rodríguez, Yolanda; Zambrano-Galván, Graciela


    Purpose To determine the frequency and association of polymorphisms in the TP53 and RB1 genes with clinical characteristics in a group of children with retinoblastoma (RB) in northern Mexico. Methods A prospective, longitudinal, and analytical study of 11 patients diagnosed with RB was conducted. Endpoint PCR and high-resolution real-time PCR were performed. Chi-square and Student t tests were used to evaluate associations between variables. Allelic frequencies, as well as genotypic and Hardy–Weinberg equilibriums, were evaluated using Guo and Thompson’s method. Results We found a statistically significant difference between the polymorphism RB1-GG/rs9568036 and tumor chemoresistance (p<0.05). The allelic variants RB1-AA and AG/rs9568036 were determined to be associated with tumor chemosensitivity (p<0.05). A statistically significant relation between the polymorphism RB1-GG/rs9568036 and males (p = 0.0386), rate ratio (RR) = 2.0 (95% confidence interval [CI] = 0.76–5.32), as well as between the allelic variants RB1-AA and AG/rs9568036 and females (p = 0.0027), RR = 8.0 (95% CI = 1.28–50.04), was observed. We also observed a statistically significant association between the rs1042522 polymorphism in the TP53 gene and unilateral presentation of the disease. Conclusions The rs9568036 polymorphism in the RB1 gene and the allelic variants can be associated with type of response to medical therapy and associated with male sex, while the allelic variant rs1042522 polymorphism in the TP53 gene is associated with the unilateral presentation of the disease in a group of Mexican children with RB. PMID:28210099

  14. Generation of induced pluripotent stem cells (iPSCs from a retinoblastoma patient carrying a c.2663G>A mutation in RB1 gene

    Sicong Zeng


    Full Text Available Skin fibroblasts were obtained from a male patient diagnosed with retinoblastoma (RB carrying a c.2663G>A mutation in the 25 exon of RB1 gene. RB-iPS cells was generated via delivered four reprogramming factors (OCT4, SOX2, NANOG and LIN28 into these skin fibroblasts. The RB-iPS cells retained the RB1 heterozygous mutation resulted in a truncated RB1 mRNA. Characteristic tests proved that the iPSC line presented typical markers of pluripotency and had the capability to form the three germ layers in vitro.

  15. Synthesis and Single Crystal Structure of RbEr2Cu3Se5

    曾卉一; 董振超; 等


    Single crystals of a new quaternary rare-earth selenide RbEr2Cu3Se5 have been isolated through the RbCl flux reaction in the RE-Cu-Se system. The title compound crystallizes in an orthorhombic system, space group Cmcm with a = 4.089(2), b = 14.498(6), c = 16.977(2)A, V = 1006.5(7)A3, Z = 4, Dc = 6.63 g/cm3, F(000) = 1720 and (MoKa) = 45.51 mm-1. The final R = 0.0498 and wR = 0.0734 for 1401 observed reflections with I > 3σ(I. The structure of RbEr2Cu3Se5 is a three-dimensional tunnel structure composed of ErSe6 and CuSe4 polyhedra with the charge-balanced Rb+ cations stuffing into the one-dimensional channels along the a direction. In the Er2RbCu3Se5 structure, the [Er2Se(1)4/2Se(2)2Se(3)4/2] double-octahedral chains are linked into a [Er2Cu2Se6] layer in the a-b plane via sharing Se1-Se3 edges with the [Cu(2)2Se(1)2Se(3)4/2] double tetrahedral chains, and [Er2Cu2Se6] layers are further interconnected along the c direction by sharing Se(1)-Se(2) edges with the [Cu(1)Se(1)2Se(2)2/2] tetrahedral chains, forming a three-dimensional framework with the channels along the a axis accommodated by Rb+ ions.

  16. Allele mining in the gene pool of wild Solanum species for homologues of late blight resistance gene RB/Rpi-blb1

    Solanum bulbocastanum comprising a CC-NBS-LRR gene RB/Rpi-blb1 confers broad-spectrum resistance to Phytophthora infestans and is currently employed in potato breeding for durable late blight (LB) resistance. Genomes of several Solanum species were reported to contain RB homologues with confirmed b...

  17. RbZnFe(PO4)2: synthesis and crystal structure

    Badri, Abdessalem; Ben Amara, Mongi


    A new iron phosphate, rubidium zinc iron(III) phosphate, RbZnFe(PO4)2, has been synthesized as single crystals by the flux method. This compound is isostructural to the previously reported KCoAl(PO4)2 [Chen et al. (1997 ▸). Acta Cryst. C53,1754–1756]. Its structure consists of a three-dimensional framework built up from corner-sharing PO4 and (Zn,Fe)O4 tetra­hedra. This mode of linkage forms channels parallel to the [100], [010] and [001] directions in which the Rb+ ions are located. PMID:27536385

  18. Diverse chromatin remodeling genes antagonize the Rb-involved SynMuv pathways in C. elegans.

    Mingxue Cui


    Full Text Available In Caenorhabditis elegans, vulval cell-fate specification involves the activities of multiple signal transduction and regulatory pathways that include a receptor tyrosine kinase/Ras/mitogen-activated protein kinase pathway and synthetic multivulva (SynMuv pathways. Many genes in the SynMuv pathways encode transcription factors including the homologs of mammalian Rb, E2F, and components of the nucleosome-remodeling deacetylase complex. To further elucidate the functions of the SynMuv genes, we performed a genome-wide RNA interference (RNAi screen to search for genes that antagonize the SynMuv gene activities. Among those that displayed a varying degree of suppression of the SynMuv phenotype, 32 genes are potentially involved in chromatin remodeling (called SynMuv suppressor genes herein. Genetic mutations of two representative genes (zfp-1 and mes-4 were used to further characterize their positive roles in vulval induction and relationships with Ras function. Our analysis revealed antagonistic roles of the SynMuv suppressor genes and the SynMuv B genes in germline-soma distinction, RNAi, somatic transgene silencing, and tissue specific expression of pgl-1 and the lag-2/Delta genes. The opposite roles of these SynMuv B and SynMuv suppressor genes on transcriptional regulation were confirmed in somatic transgene silencing. We also report the identifications of ten new genes in the RNAi pathway and six new genes in germline silencing. Among the ten new RNAi genes, three encode homologs of proteins involved in both protein degradation and chromatin remodeling. Our findings suggest that multiple chromatin remodeling complexes are involved in regulating the expression of specific genes that play critical roles in developmental decisions.

  19. IL12RB2 gene is associated with the age of type 1 diabetes onset in Croatian family Trios.

    Marina Pehlić

    Full Text Available BACKGROUND: Common complex diseases are influenced by both genetic and environmental factors. Many genetic factors overlap between various autoimmune diseases. The aim of the present study is to determine whether four genetic variants known to be risk variants for several autoimmune diseases could be associated with an increased susceptibility to type 1 diabetes mellitus. METHODS AND FINDINGS: We genotyped four genetic variants (rs2358817, rs1049550, rs6679356, rs9865818 within VTCN1, ANXA11, IL12RB2 and LPP genes respectively, in 265 T1DM family trios in Croatian population. We did not detect association of these polymorphisms with T1DM. However, quantitative transmission disequilibrium test (QTDT, orthogonal model revealed a significant association between the age of onset of T1DM and IL12RB2 rs6679356 variant. An earlier onset of T1DM was associated with the rs6679356 minor dominant allele C (p = 0.005. The association remained significant even after the Bonferroni correction for multiple testing and permutation. CONCLUSIONS: Variants originally associated with juvenile idiopathic arthritis (VTCN1 gene, sarcoidosis (ANXA11 gene, primary biliary cirrhosis (IL12RB2 gene and celiac disease (LPP gene were not associated with type 1 diabetes in our dataset. Nevertheless, association of IL12RB2 rs6679356 polymorphism with the age of T1DM onset suggests that this gene plays a role in defining the time of disease onset.

  20. Electronic structure of β-RbNd(MoO4)2 by XPS and XES

    Atuchin, V. V.; Khyzhun, O. Y.; Chimitova, O. D.; Molokeev, M. S.; Gavrilova, T. A.; Bazarov, B. G.; Bazarova, J. G.


    β-RbNd(MoO4)2 microplates have been prepared by the multistage solid state synthesis method. The phase composition and micromorphology of the final product have been evaluated by XRD and SEM methods. The electronic structure of β-RbNd(MoO4)2 molybdate has been studied employing the X-ray photoelectron spectroscopy (XPS) and X-ray emission spectroscopy (XES). For the molybdate, the XPS core-level and valence-band spectra, as well as XES bands representing energy distribution of the Mo 4d- and O 2p-like states, have been measured. It has been established that the O 2p-like states contribute mainly to the upper portion of the valence band with also significant contributions throughout the whole valence-band region. The Mo 4D-like states contribute mainly to a lower valence band portion.

  1. Post-transcriptional gene expression control by NANOS is up-regulated and functionally important in pRb-deficient cells.

    Miles, Wayne O; Korenjak, Michael; Griffiths, Lyra M; Dyer, Michael A; Provero, Paolo; Dyson, Nicholas J


    Inactivation of the retinoblastoma tumor suppressor (pRb) is a common oncogenic event that alters the expression of genes important for cell cycle progression, senescence, and apoptosis. However, in many contexts, the properties of pRb-deficient cells are similar to wild-type cells suggesting there may be processes that counterbalance the transcriptional changes associated with pRb inactivation. Therefore, we have looked for sets of evolutionary conserved, functionally related genes that are direct targets of pRb/E2F proteins. We show that the expression of NANOS, a key facilitator of the Pumilio (PUM) post-transcriptional repressor complex, is directly repressed by pRb/E2F in flies and humans. In both species, NANOS expression increases following inactivation of pRb/RBF1 and becomes important for tissue homeostasis. By analyzing datasets from normal retinal tissue and pRb-null retinoblastomas, we find a strong enrichment for putative PUM substrates among genes de-regulated in tumors. These include pro-apoptotic genes that are transcriptionally down-regulated upon pRb loss, and we characterize two such candidates, MAP2K3 and MAP3K1, as direct PUM substrates. Our data suggest that NANOS increases in importance in pRb-deficient cells and helps to maintain homeostasis by repressing the translation of transcripts containing PUM Regulatory Elements (PRE).

  2. Presence of the potato late blight resistance gene RB does not promote adaptive parasitism of phytophthora infestans

    The gene RB is derived from the wild potato species S. bulbocastanum and confers partial resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. In order to investigate whether a single strain of P. infestans can adapt to overcome this partial resistance source, we subject...

  3. Synthesis, X-ray Crystal Structure and Thermal Decomposition Mechanism of [RbHTNR]∞

    ZHENG, Hong; ZHANG, Tong-Lai; ZHANG, Jian-Guo; QIAO, Xiao-Jing; YANG, Li; YU, Kai-Bei


    A new compound, [RbHTNR]∞ [HTNR-: C6H(NO2)3(OH)O ], was synthesized by the reaction of rubidium nitrate and styphnic acid. The molecular structure was characterized using X-ray diffraction analysis, elemental analysis and FTIR spectroscopy. The crystalline is monoclinic with space group P21/n and the empirical formula C6H2N3OsRb. The unit cell parameters are: a=0.4525 nm, b=1.0777 nm, c= 1.9834 nm, β=90.47(2)°, V=0.96725 nm3, Z=4, Dc=2.263 g/cm3, Mr=329.58, F(000)=640, μ(Mo Kα)=5.165 mm-1. The thermal decomposition mechanism of the complex was studied by differential scanning calorimetry (DSC), thermogravimetryderivative thermogravimetry (TG-DTG) and FTIR techniques. At the linear rate of 10 ℃/min, the thermal decomposition of the complex showed three mass reducing processes between 60 and 500 ℃, and finally evolved RbCN and some gaseous products.

  4. High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

    Pham, Van-Thai; Fulton, John L.


    In concentrated solutions of aqueous RbCl, all of the Rb+ and Cl- ions exist as contact ion pairs. This full structural assessment is derived from the refinement of three independent experimental measurements: the Rb and Cl K-edge x-ray absorption fine structure (XAFS) and the x-ray diffraction spectra (XRD). This simultaneous refinement of the XAFS and XRD data provides high accuracy since each method probes the structure of different local regions about the ions with high sensitivity. At high RbCl concentration (6 m (mol/kg )) the solution is dominated by Rb+ - Cl- contact ion pairs yielding an average of 1.5 pairs at an Rb-Cl distance of 3.24 Å. Upon formation of these ion pairs, approximately 1.1 waters molecules are displaced from the Rb+ and 1.4 water molecules from Cl-. The hydration shells about both the cation and anion are also determined. These results greatly improve the understanding of monovalent ions and provide a basis for testing the Rb+-Cl- interaction potentials used in molecular dynamics (MD) simulation. This research was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  5. Measurement of hyperfine structure in the $\\rm D_1$ line of $^{87}$Rb

    Datar, Durgesh; Ananthamurthy, Sharath; Natarajan, Vasant


    This work reports a new measurement of the hyperfine structure constant of the $\\rm D_1 $ line in $ \\rm ^{87}Rb $ through precision laser spectroscopy. In a departure from methods that rely on locking the laser on the transitions of interest, the technique reported here relies on scanning around the transition. This is carried out so as to overcome potential frequency shifts caused by various noise sources including electronic noise and thermal fluctuations. The value of the hyperfine constant reported here is $ A = 408.29(25) $ MHz, which is in variance from an earlier value reported from our lab but is consistent with other recent measurements.

  6. Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

    Bogdan C Paun

    Full Text Available BACKGROUND: Coding region microsatellite instability (MSI results in loss of gene products and promotion of microsatellite-unstable (MSI-H carcinogenesis. Recent studies have indicated that MSI within 3'-untranslated regions (3'UTRs may post-transcriptionally dysregulate gene products. Within this context, we conducted a broad mutational survey of 42 short 3'UTR microsatellites (MSs in 45 MSI-H colorectal tumors and their corresponding normal colonic mucosae. METHODOLOGY/PRINCIPAL FINDINGS: In order to estimate the overall susceptibility of MSs to MSI in MSI-H tumors, the observed MSI frequency of each MS was correlated with its length, interspecies sequence conservation level, and distance from some genetic elements (i.e., stop codon, polyA signal, and microRNA binding sites. All MSs were stable in normal colonic mucosae. The MSI frequency at each MS in MSI-H tumors was independent of sequence conservation level and distance from other genetic elements. In contrast, MS length correlated significantly with MSI frequency in MSI-H tumors (r=0.86, p=7.2x10(-13. 3'UTR MSs demonstrated MSI frequencies in MSI-H tumors higher than the 99% upper limit predicted by MS length for RB1-inducible coiled-coil 1(RB1CC1, mutation frequency 68.4%, NUAK family SNF1-like kinase 1(NUAK1, 31.0%, and Rtf1, Paf1/RNA polymerase II complex component, homolog (RTF1, 25.0%. An in silico prediction of RNA structure alterations was conducted for these MSI events to gauge their likelihood of affecting post-transcriptional regulation. RB1CC1 mutant was predicted to lose a microRNA-accessible loop structure at a putative binding site for the tumor-suppressive microRNA, miR-138. In contrast, the predicted 3'UTR structural change was minimal for NUAK1- and RTF1 mutants. Notably, real-time quantitative RT-PCR analysis revealed significant RB1CC1 mRNA overexpression vs. normal colonic mucosae in MSI-H cancers manifesting RB1CC1 3'UTR MSI (9.0-fold; p = 3.6x10(-4. CONCLUSIONS: This

  7. Rietveld refinement of the crystal structures of Rb2XSi5O12 (X = Ni, Mn

    Anthony M. T. Bell


    Full Text Available The synthetic leucite silicate framework mineral analogues Rb2XSi5O12 {X = Ni [dirubidium nickel(II pentasilicate] and Mn [dirubidium manganese(II pentasilicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetrahedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb+ cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetrahedrally coordinated sites (T-sites. However, the Ni displacement parameter and the Ni—O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder.

  8. P53 and Rb tumor suppressor gene alterations in gastric cancer Alterações dos genes supressores tumorais p53 e Rb no câncer gástrico

    Rejane Mattar


    Full Text Available Inactivation of tumor suppressor genes has been frequently observed in gastric carcinogenesis. Our purpose was to study the involvement of p53, APC, DCC, and Rb genes in gastric carcinoma. METHOD: Loss of heterozygosity of the p53, APC, DCC and Rb genes was studied in 22 gastric cancer tissues using polymerase chain reaction; single-strand conformation polymorphism of the p53 gene exons 5-6 and exons 7-8 was studied using 35S-dATP, and p53 expression was detected using a histological immunoperoxidase method with an anti-p53 clone. RESULTS AND DISCUSSION: No loss of heterozygosity was observed in any of these tumor suppressor genes; homozygous deletion was detected in the Rb gene in 23% (3/13 of the cases of intestinal-type gastric carcinoma. Eighteen (81.8% cases showed band mobility shifts in exons 5-6 and/or 7-8 of the p53 gene. The presence of the p53 protein was positive in gastric cancer cells in 14 cases (63.6%. Normal gastric mucosa showed negative staining for p53; thus, the immunoreactivity was likely to represent mutant forms. The correlation of band mobility shift and the immunoreactivity to anti-p53 was not significant (P = .90. There was no correlation of gene alterations with the disease severity. CONCLUSIONS: The inactivation of Rb and p53 genes is involved in gastric carcinogenesis in our environment. Loss of the Rb gene observed only in the intestinal-type gastric cancer should be further evaluated in association with Helicobacter pylori infection. The p53 gene was affected in both intestinal and diffuse histological types of gastric cancer.A inativação de genes supressores tumorais tem sido freqüentemente observada na carcinogênese gástrica. O nosso objetivo foi estudar o envolvimento dos genes p53, APC, DCC e Rb no câncer gástrico. MÉTODO: Vinte e dois casos de câncer gástrico foram estudados por PCR-LOH (reação de polimerase em cadeia- perda de alelo heterozigoto dos genes p53, APC, DCC e Rb; e por PCR-SSCP (rea

  9. Rb1 gene inactivation expands satellite cell and postnatal myoblast pools.

    Hosoyama, Tohru; Nishijo, Koichi; Prajapati, Suresh I; Li, Guangheng; Keller, Charles


    Satellite cells are well known as a postnatal skeletal muscle stem cell reservoir that under injury conditions participate in repair. However, mechanisms controlling satellite cell quiescence and activation are the topic of ongoing inquiry by many laboratories. In this study, we investigated whether loss of the cell cycle regulatory factor, pRb, is associated with the re-entry of quiescent satellite cells into replication and subsequent stem cell expansion. By ablation of Rb1 using a Pax7CreER,Rb1 conditional mouse line, satellite cell number was increased 5-fold over 6 months. Furthermore, myoblasts originating from satellite cells lacking Rb1 were also increased 3-fold over 6 months, while terminal differentiation was greatly diminished. Similarly, Pax7CreER,Rb1 mice exhibited muscle fiber hypotrophy in vivo under steady state conditions as well as a delay of muscle regeneration following cardiotoxin-mediated injury. These results suggest that cell cycle re-entry of quiescent satellite cells is accelerated by lack of Rb1, resulting in the expansion of both satellite cells and their progeny in adolescent muscle. Conversely, that sustained Rb1 loss in the satellite cell lineage causes a deficit of muscle fiber formation. However, we also show that pharmacological inhibition of protein phosphatase 1 activity, which will result in pRb inactivation accelerates satellite cell activation and/or expansion in a transient manner. Together, our results raise the possibility that reversible pRb inactivation in satellite cells and inhibition of protein phosphorylation may provide a new therapeutic tool for muscle atrophy by short term expansion of the muscle stem cells and myoblast pool.

  10. Caenorhabditis elegans lin-35/Rb, efl-1/E2F and other synthetic multivulva genes negatively regulate the anaphase-promoting complex gene mat-3/APC8.

    Garbe, David; Doto, Jeffrey B; Sundaram, Meera V


    Retinoblastoma (Rb)/E2F complexes repress expression of many genes important for G(1)-to-S transition, but also appear to regulate gene expression at other stages of the cell cycle. In C. elegans, lin-35/Rb and other synthetic Multivulva (SynMuv) group B genes function redundantly with other sets of genes to regulate G(1)/S progression, vulval and pharyngeal differentiation, and other unknown processes required for viability. Here we show that lin-35/Rb, efl-1/E2F, and other SynMuv B genes negatively regulate a component of the anaphase-promoting complex or cyclosome (APC/C). The APC/C is a multisubunit complex that promotes metaphase-to-anaphase progression and G(1) arrest by targeting different substrates for ubiquitination and proteasome-mediated destruction. The C. elegans APC/C gene mat-3/APC8 has been defined by temperature-sensitive embryonic lethal alleles that strongly affect germline meiosis and mitosis but only weakly affect somatic development. We describe severe nonconditional mat-3 alleles and a hypomorphic viable allele (ku233), all of which affect postembryonic cell divisions including those of the vulval lineage. The ku233 lesion is located outside of the mat-3 coding region and reduces mat-3 mRNA expression. Loss-of-function alleles of lin-35/Rb and other SynMuv B genes suppress mat-3(ku233) defects by restoring mat-3 mRNA to wild-type levels. Therefore, Rb/E2F complexes appear to repress mat-3 expression.

  11. Structural and optoelectronic properties of cubic perovskite RbPbF3

    K Ephraim Babu; N Murali; D Tirupathi Swamy; V Veeraiah


    The structural and optoelectronic properties of cubic perovskite RbPbF 3 are calculated using all electrons full potential linearized augmented plane wave (FP-LAPW) method. The calculated lattice constant is in good agreement with the experimental result. The calculated band structure shows a direct band gap of 3.07 eV. The contribution of different bands is analysed from the total and partial density of state curves. We identified hybridization of Pb , Pb states with F states in the valence bonding region. Calculations of the optical spectra, viz., the dielectric function, optical reflectivity, absorption coefficient, real part of optical conductivity, refractive index, extinction coefficient and electron energy loss are performed for the energy range of 0-30 eV. Based on the direct bandgap, as well as other optical properties of the compound, it is predicted that this material is useful for vacuum-ultraviolet-transparent (VUV-transparent) applications.

  12. Prognostic implications of RB1 tumour suppressor gene alterations in the clinical outcome of human osteosarcoma: a meta-analysis.

    Ren, W; Gu, G


    Primary osteosarcoma is the most frequent malignant bone cancer in children and teenagers. Genetic alterations at the retinoblastoma 1 (RB1) gene has been implicated in the development and progression of human osteosarcoma. Here, we performed a meta-analysis to examine the impact of RB1 mutations on the survival of osteosarcoma patients, the risk of metastasis and the histological response of osteosarcoma to chemotherapy. A systemic review of the Medline, Embase, Scopus and Cochrane Library yielded 12 eligible studies with 491 patients for this study. Forest plots resulting from our meta-analyses illustrate that loss of RB1 function results in a 1.62-fold increase in the mortality rate for osteosarcoma patients (RR = 1.62, 95% CI: 1.23-2.13; Z = 3.44, P = 0.0006), a significant increase in osteosarcoma metastasis (OR = 3.95, 95% CI: 1.86-8.38; Z = 3.57; P = 0.0004), and a significant reduction in the histological response of osteosarcoma to chemotherapy (OR = 0.35; 95% CI: 0.13-0.94; Z = -2.08; P = 0.038). Additionally, the nearly symmetrical funnel plot (Egger's test, t = 1.15, P = 0.288) indicates absence of publication bias regarding the meta-analysis that examined the correlation of RB1 alterations with the survival rate for osteosarcoma patients. Our findings suggest that RB1 alterations may serve as a prognostic marker for the management of osteosarcoma patients. © 2015 John Wiley & Sons Ltd.

  13. Magnetic structure and bonding of rare-earth diboride compounds RB{sub 2}: First-principles calculations

    Kacimi, S.; Zazoua, F.; Djermouni, M.; Zaoui, A. [Modelling and Simulation in Materials Science Laboratory, Djillali Liabes University of Sidi Bel-Abbes, Sidi Bel-Abbes 22000 (Algeria); Bekkouche, B. [Signals and Systems Laboratory, Abdelhamid Ibn Badis University of Mostaganem, Mostaganem 27000 (Algeria); Boukortt, A. [Elaboration Characterization Physico-Mechanics of Materials and Metallurgical Laboratory ECP3M, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University of Mostaganem, Mostaganem 27000 (Algeria)


    The electronic structure and magnetic behavior of hexagonal rare-earth diboride RB{sub 2} are studied using ab initio density-functional theory in the DFT + U approach. The effect of the spin-orbit coupling is also investigated and it is found to be a necessary requirement for the accurate description of the magnetic moment. In this paper, we study the magnetic phase stability of RB{sub 2} compounds; the band structure and the density of state (DOS) results prove that the coulomb potential and the spin-orbit interaction are keys factors to understand the magnetic properties of these series of materials. In addition, we also explain the behavior of a chemical bond of RB{sub 2} compounds through the analysis of the DOS and of the charge density. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Mutation of purD and purF genes further attenuates Brucella abortus strain RB51.

    Truong, Quang Lam; Cho, Youngjae; Barate, Abhijit Kashinath; Kim, Suk; Watarai, Masahisa; Hahn, Tae-Wook


    In the present study, transposon mutagenesis was used to further attenuate Brucella abortus RB51 vaccine strain. Two purD and purF mutants were constructed, characterized and evaluated for attenuation via intracellular survival in murine macrophage-like RAW264.7 and HeLa cells, and by clearance in BALB/c mice. The purD and purF mutants showed significantly decreased intracellular survival, and complementation of these mutants with intact copies of purD or purF genes of RB51 strain was able to restore these defects. In addition, the pur mutants presented significantly lowered persistence in mice. Immunization with purD and purF mutants protected mice against a challenge with the virulent B. abortus strain 544 at a level similar to that of the parent RB51. These data suggest that genes encoding the early stages of purine biosynthesis (purD and purF) are required for intracellular survival and virulence of B. abortus.

  15. Insight into the architecture of the NuRD complex: structure of the RbAp48-MTA1 subcomplex.

    Alqarni, Saad S M; Murthy, Andal; Zhang, Wei; Przewloka, Marcin R; Silva, Ana P G; Watson, Aleksandra A; Lejon, Sara; Pei, Xue Y; Smits, Arne H; Kloet, Susan L; Wang, Hongxin; Shepherd, Nicholas E; Stokes, Philippa H; Blobel, Gerd A; Vermeulen, Michiel; Glover, David M; Mackay, Joel P; Laue, Ernest D


    The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex.

  16. Syntheses and Structures of the New Quaternary Rubidium Selenides Rb Ln2CuSe 4 ( Ln=Sm, Gd, Dy), Rb 1.5Ln2Cu 2.5Se 5 ( Ln=Gd, Dy), and RbSm 2Ag 3Se 5

    Huang, Fu Qiang; Ibers, James A.


    Six quaternary rubidium selenides RbLn2CuSe4 (Ln=Sm, Gd, Dy), Rb1.5Ln2Cu2.5Se5 (Ln=Gd, Dy), and RbSm2Ag3Se5 have been synthesized at 1073 K with the use of a reactive flux of Rb2Se3. At 153 K all compounds contain four formula units in orthorhombic unit cells. The isostructural compounds RbLn2CuSe4 crystallize in space group Cmcm; the isostructural compounds Rb1.5Ln2Cu2.5Se5 crystallize in space group Pnnm; RbSm2Ag3Se5 crystallizes in space group Cmcm. The cells of RbLn2CuSe4 are (Ln, a, b, c (Å)): Sm, 4.1834(9), 14.308(3), 14.439(3); Gd, 4.1568(8), 14.227(3), 14.409(3); Dy, 4.1237(10), 14.083(4), 14.291(3), and the corresponding R1 indices for the refined structures are 0.023, 0.029, and 0.039. The cells of Rb1.5Ln2Cu2.5Se5 are: Gd, 16.243(3), 16.449(3), 4.0980(7); Dy, 16.120(3), 16.292(3), 4.0610(8), and the R1 indices are 0.036 and 0.043. The cell of RbSm2Ag3Se5 is 4.3223(6), 15.229(2), 17.420(3) Å and the R1 index is 0.025. All six are closely related three-dimensional tunnel structures. Their anionic frameworks are built from LnSe6 octahedra and MSe4 (M=Cu, Ag) tetrahedra. RbLn2CuSe4 contains infinite 1∞[CuSe3] chains of vertex-sharing tetrahedra; Rb1.5Ln2Cu2.5Se5 also contains infinite chains of tetrahedra; and the tunnel in RbSm2Ag3Se5 holds one Rb+ cation in a 10-membered ring consisting of six Ag-Se bonds and four Sm-Se bonds. Rb1.5Dy2Cu2.5Se5, which is paramagnetic, obeys the Curie-Weiss law and has an effective magnetic moment of 10.63(4) μB.

  17. Correlation of the properties of ionic conductivity-structure for the RbGaO2 solid electrolyte

    Proskurnina, N. V.; Voronin, V. I.; Berger, I. F.; Shekhtman, G. Sh.


    The crystal structure of rubidium gallate RbGaO2 in the temperature range of 300-853 K has been investigated using high-temperature neutron diffraction. The channels available for the motion of rubidium cations in the low-temperature and high-temperature modifications of RbGaO2 have been determined using the computer simulation with the TOPOS program. A correlation between the radius of the migration channel cross section and the rubidium cation conductivity has been established.

  18. Magnetic and structural characterization of the 2D XY-ferromagnet Rb2CrCl2I2 (abstract)

    Visser, D.; Bramwell, S. T.; Kremer, R. K.


    Rb2CrCl2I2 crystallizes with a Jahn-Teller deformed K2NiF4 structure. This results in a ferromagnetic behavior for this compound. Rb2CrCl2I2 orders ferromagnetically at Tc=56.9(2) K. Magnetization and magnetic susceptibility measurements, using a vibrating sample magnetometer, Faraday balance, and SQUID magnetometer, on polycrystalline samples were used for the magnetic characterization. Rb2CrCl2I2 shows a Curie-Weiss behavior between 150 and 300 K. The intraplanar superexchange constant J/k=5.8 K. The intra- and interplanar anisotropy have been obtained from the magnetization curves at 4.2 K and are estimated at Hintra=0.16(2) T and Hinter=4.5(2) T.

  19. Effect of Exogenous p16ink4a and hRb1 Genes on Cell Cycle Regulation of Osteosarcoma Cell

    LIAO Xiang; YANG Shuhua; SHAO Zengwu; LI Jin; LIU Yong; XIONG Xiaoqian; LIU Xin


    To study the effect on regulation of cell cycle of osteosarcoma cell line MG63 tranceduced with exogenous p16ink4a and hRb1 genes, pIRES-p16ink4a-hRb1, pIRES-p16ink4a and pIRES-hRb1 plasmids were constructed by gene recombination technology. The recombinant plasmid was transferred into osteosarcoma cell line MG63 by metafectene, and the resistant clones were selected by G418 selective medium. mRNA and protein expression of osteosarcoma cell line were assayed by RT-PCR and Western Blot respectively. Cell cycle and apoptosis were analyzed by subG1 flow cytometric. Cell proliferation was tested by MTT. In the genome of these transfected target cells, the expression of p16ink4a and hRb1 mRNA and protein were detected respectively in vitro. It was demonstrated with subG1 flow cytometric analysis and MTT method that p16ink4a and hRb1 genes cooperation more significantly inhibited cell growth and induced a more marked G1 arrest and apoptosis than p16ink4a/hRb1 alone (P<0.01). Coexpression of exogenous p16ink4a with hRb1 broke the regulatory feedback loop of p16ink4a-cyclinD1/CDK-hRb1 and played a more significant role in inhibiting cell growth as well as inducing cell apoptosis than p16ink4a or hRb1 did alone in vitro.

  20. Synthesis, crystal structure and high-temperature transport properties of the new cluster compound Rb2Mo15Se19

    Daigre, Gilles; Gougeon, Patrick; Gall, Philippe; Gautier, Régis; Guillou, Olivier; Vaney, Jean-Baptiste; Candolfi, Christophe; Dauscher, Anne; Lenoir, Bertrand


    We report on the synthesis, crystal structure and high-temperature transport properties of Rb2Mo15Se19, a new member of the large family of M2Mo15Se19 (M=In, Tl, K, Ba) cluster compounds. Polycrystalline samples and single crystals of the ternary selenide Rb2Mo15Se19 were obtained by solid-state reactions. The trigonal crystal structure, successfully refined in space group R 3 bar c (No. 167) with unit-cell parameters a=9.7618(1) Å, c=58.254(1) Å and Z=6, was determined by single-crystal X-ray diffraction. The crystal structure contains Mo6 Se8i Se6a and Mo9Se11iSe6a cluster units in equal proportion and separated from each other by large voids, which are filled up by Rb atoms. Measurements of the electrical resistivity, thermopower and thermal conductivity revealed that Rb2Mo15Se19 behaves as a p-type metal with relatively low electrical resistivity and thermopower. Despite its complex crystal structure, the lattice thermal conductivity that amounts to 1.3 W m-1 K-1 at 300 K is significantly higher than in Ag-filled analogues, which provides possible guidelines to enhance its thermoelectric properties.

  1. First-principle study on bulk and (1 1 1) surface of MP (M = K and Rb) in rocksalt structure

    Gao, Qiang; Li, Lei; Xie, Huan-Huan; Lei, Gang; Deng, Jian-Bo; Hu, Xian-Ru, E-mail:


    The electronic and magnetic properties of bulk and (1 1 1) surfaces for MP (M = K and Rb) in rocksalt structure have been investigated by employing first-principle calculations. The results reveal that the compounds are half-metallic ferromagnets at the equilibrium lattice constants with large half-metallic band gaps of 0.46 and 0.74 eV. The (1 1 1) surfaces of KP and RbP keep their bulk half-metallic property. We study the stabilities of the bulk compounds and their (1 1 1) surfaces as well. The results show that those bulk compounds are more stable in the rocksalt structure than in the tetragonal structure. In addition, the K- and Rb-terminated surfaces are more stable than their P-terminated surfaces. - Highlights: • The half metallic properties of rocksalt-type KP and RbP are studied. • The Slater-Pauling behaviours, energy levels and fat-bands of them are discussed. • The properties to KP's and RBP's (1 1 1) surfaces have been investigated. • The stabilities of bulk compounds and surfaces are studied.

  2. Ethnic variations of a retinoblastoma susceptibility gene (RB1) polymorphism in eight Asian populations

    Priya Kadam-Pai; Xin-Yi Su; Jasmin Jiji Miranda; Agustinus Soemantri; Nilmani Saha; Chew-Kiat Heng; Poh-San Lai


    An A → G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. The RB1 SNP was present in all populations at an overall frequency of ≤ 0.18. Heterozygosity was higher in the Southeast Asian groups (0.14–0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04–0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. This RB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studying RB1 inheritance by pedigree analysis.

  3. Expression of pRb2/p130 Gene in Human Endometrial Carcinoma Cells and the Significance%子宫内膜癌中pRb2/p130的表达及意义

    支霜; 傅芬


    Objective To investigate the expression of pRb2/p130 gene and its relationship with the patholgical clinical features of human endometrial carcinoma.Methods The levels of pRb2/P130 protein were examined with immunohistochemical SP method in 28 smples of normal endometrial tissue,20 samples of atypical endometrial hyperplasia and 30 samples of endometrial adenocarcinomas.Results The positive rate of pRb2/p130 protein in the normal endometrium,atypical endometrial hyperplasia cells and endometrial adenocarcinoma cells was respectively 82.1%,55.0% and 23.3%.pRb2/p130 protein in endometrial atypical hyperplasia or endometrial adenocarcinoma was significantly lower than that in the normal tissue (P0.05).Conclusion Descent or deletion of the expression of pRb2/p130 gene is of a frequent incidence in human endometrial carcinoma.The positive rate of pRb2/p130 expression is reversly proportionate to malignant degree of endometrial carcinoma,which indicats that pRb2/p130 plays an important role in the development and pathogenesis of endometrial carcinoma.%目的 探讨子宫内膜组织中pRb2/p130的表达及其与子宫内膜癌临床病理特征的关系.方法 应用免疫组化SP法检测pRb2/p130在28例正常增生期子宫内膜、20例不典型增生子宫内膜、30例子宫内膜腺癌组织中的表达.结果 pRb2/p130阳性表达率在正常增生期子宫内膜、不典型增生子宫内膜、子宫内膜腺癌组织中依次递减(分别为82.1%、55.0%、23.3%),且子宫内膜腺癌和不典型性增生中明显低于正常增生期子宫内膜,差异均有统计学意义(P0.05).结论 在子宫内膜癌中pRb2/p130的表达下降或缺失是一个频发事情,其恶性度愈高阳性率愈低,提示pRb2/p130与子宫内膜癌的发生、发展密切相关,并在其发病机制中起着重要的作用.

  4. Abnormalities in structure and expression of the retinoblastoma gene in small cell lung cancer cell lines and xenografts in nude mice

    Rygaard, K; Sorenson, G D; Pettengill, O S


    the Rb protein, we investigated the expression of the Mr 110,000-116,000 Rb protein in SCLC tumors grown as xenografts in nude mice and/or as cell lines. Rb messenger RNA expression was determined by Northern blotting, and gross structural gene alterations were investigated by Southern blotting. Tumors...... small cell lung cancer (SCLC). Absence of the 4.7 kilobase mRNA has been found to be frequent in SCLC, and it has been reported that the Rb Mr 110,000-116,000 protein product is always absent, even in tumors expressing Rb mRNA. Using Western blotting technique with a monoclonal antibody directed against...

  5. Data of evolutionary structure change: 1E1RB-2HLDT [Confc[Archive


  6. Splicing aberrations caused by constitutional RB1 gene mutations in retinoblastoma

    Vidya Latha Parsam; Mohammed Javed Ali; Santosh G Honavar; Geeta K Vemuganti; Chitra Kannabiran


    Analysis of RB1 mRNA from blood leukocytes of patients with retinoblastoma identified the effects of mutations involving consensus splice site, exonic substitution and whole-exon deletions identified in genomic DNA of these patients. In addition, this study identified mutations in cases in which no mutations were detectable in the genomic DNA. One proband had mutation at the canonical splice site at +5 position of IVS22, and analysis of the transcripts in this family revealed skipping of exon 22 in three members of this family. In one proband, a missense substitution of c.652T > G (g.56897T > G; Leu218Val) in exon 7 led to splicing aberrations involving deletions of exons 7 and 8, suggesting the formation of a cryptic splice site. In two probands with no detectable changes in the genomic DNA upon screening of RB1 exons and flanking intronic sequences, transcripts were found to have deletions of exon 6 in one, and exons 21 and 22 in another family. In two probands, RNA analysis confirmed genomic deletions involving one or more exons. This study reveals novel effects of RB1 mutations on splicing and suggests the utility of RNA analysis as an adjunct to mutational screening of genomic DNA in retinoblastoma.

  7. First-principles calculation of the structural, electronic, and magnetic properties of cubic perovskite RbXF3 (X = Mn, V, Co, Fe)

    rehman Hashmi, Muhammad Raza ur; Zafar, Muhammad; Shakil, M.; Sattar, Atif; Ahmed, Shabbir; Ahmad, S. A.


    First-principles calculations by means of the full-potential linearized augmented plane wave method using the generalized gradient approximation with correlation effect correction (GGA+U) within the framework of spin polarized density functional theory (DFT+U) are used to study the structural, electronic, and magnetic properties of cubic perovskite compounds RbXF3 (X = Mn, V, Co, and Fe). It is found that the calculated structural parameters, i.e., lattice constant, bulk modulus, and its pressure derivative are in good agreement with the previous results. Our results reveal that the strong spin polarization of the 3d states of the X atoms is the origin of ferromagnetism in RbXF3. Cohesive energies and the magnetic moments of RbXF3 have also been calculated. The calculated electronic properties show the half-metallic nature of RbCoF3 and RbFeF3, making these materials suitable for spintronic applications.

  8. Synthesis and crystal structure of new K and Rb selenido/tellurido ferrate cluster compounds

    Stueble, Pirmin; Berroth, Angela; Roehr, Caroline [Freiburg Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie


    In the course of a systematic study of alkali iron chalcogenido salts containing clusters [Fe{sub 4}Q{sub 8}] a series of new mixed-valent potassium and rubidium selenido and tellurido ferrates(II/III) was synthesized by carefully heating the pure elements enclosed in sample tubes under an argon atmosphere up to maximum temperatures of 800-900 C. Their crystal structures have been determined by means of single crystal X-ray diffraction. The mixed-valent Fe{sup II/III} tellurido ferrates A{sub 7}[Fe{sub 4}Te{sub 8}] form three different structure types. All structures contain tetramers of four edge sharing [FeTe{sub 4}] tetrahedra, which are connected by common edges to form only slightly distorted tetrahedral [Fe{sub 4}Te{sub 8}]{sup 7-} anions ('stella quadrangula') with a [Fe{sub 4}Te{sub 4}] cubane core. In all cases, these anions are surrounded by 26 alkali cations, which are located at the eight corners and the midpoints of the six faces and 12 edges of a cube. The three crystal structures can thus be described by three different packings of cuboid moieties: The monoclinic rubidium compound Rb{sub 7}[Fe{sub 4}Te{sub 8}] (space group C2/c, a = 2000.16(7), b = 897.79(3), c = 1768.12(6) pm, β = 117.4995(10) , Z = 4, R1 = 0.0296) is isotypic to the known cesium tellurido and sulfido ferrates Cs{sub 7}[Fe{sub 4}(S/Te){sub 8}]. Depending on the temperature, K{sub 7}[Fe{sub 4}Te{sub 8}] forms two different but closely related new structure types: The tetragonal r.t. modification (space group P4{sub 2}/nmc, a = 1222.25(14), c = 872.1(2) pm, Z = 2, R1 = 0.0583) crystallizes in a supergroup of the orthorhombic l.t. (100 K) form (space group Pbcn, a = 1715.5, b = 866.76(3), c = 1715.50(7) pm, Z = 4, R1 = 0.0160). In all structures, the cluster centered cubes are stacked to form columns along the short (∼ 870 pm) axis. These columns are themselves densely packed with 4 (both K compounds) and 6 (A = Rb) adjacent face-sharing columns. According to these

  9. Developmental patterns of serum leptin levels, leptin gene expression in adipose tissue and Ob-Rb gene expression in hypothalamus of Erhualian and Large White pigs

    ZHOU; Jie; ZHAO; Ruqian; WEI; Xihui; XIA; Dong; XU; Qingfu


    The present study was aimed to investigate the developmental patterns of leptin mRNA expression in dorsal subcutaneous adipose tissue and Ob-Rb mRNA expression in hypothalamus in pigs of different breeds and sexes. Erhualian gilts and boars and Large White boars were sampled at birth, 3, 20, 30, 45, 90, 120 and 180 days of age, respectively. Serum concentration of leptin was measured with RIA and single tube semi-quantitative RT-PCR was applied to determine the relative abundances of mRNA expression using 18S rRNA as an internal standard. The results showed that leptin mRNA expression in adipose tissue increased with age and displayed both sex and breed differences. In Erhualian pigs, females expressed higher leptin mRNA compared with males, and Erhualian boars showed higher abundance of leptin mRNA than Large White boars (P<0.01). Serum leptin levels were in good agreement with adipose leptin mRNA, displaying similar sex and line differences. In contrast, expression of Ob-Rb mRNA in hypothalamus exhibited a distinctive pattern, decreased gradually after birth, and then increased till weaning. After weaning, Ob-Rb gene expression decreased gradually with age but rose gradually again from 120 to 180 days of age in Erhualian pigs. The expression of Ob-Rb mRNA was higher in Large White pigs than that in Erhualian pigs (P<0.01). The results suggest that the serum leptin level and leptin gene expression in adipose tissue highly correlate with adiposity.

  10. Synthesis, crystal structure, and properties of Na{sub 2}RbAuO{sub 2}; Synthese, Kristallstruktur und Eigenschaften von Na{sub 2}RbAuO{sub 2}

    Mudring, A.V.; Jansen, M. [Max-Planck-Inst. fuer Festkoerperforschung, Stuttgart (Germany)


    Single phase samples of Na{sub 2}RbAuO{sub 2} were prepared by reacting RbAu with Na{sub 2}O{sub 2} in an equimolar ratio in sealed silver cylinders (placed under argon in glas tubes) at 400 C for two weeks. The colourless single crystals of needle shaped habitus decompose immediately when exposed to air. Na{sub 2}RbAuO{sub 2} (Pearsoncode oP12, Pnnm, a = 992.76(6), b = 559.03(3), c = 408.64(3) pm, Z = 2, 414 reflections with I{sub o} > 2{sigma}(I), R{sub 1} = 0.0363, wR{sub 2} = 0.1057) crystallizes isotypic with Na{sub 2}KAuO{sub 2}. Besides linear [O-Au-O] units, which are characteristic for oxoaurate(I), the structure reveals uncommon low coordination numbers for the alkali metal cations. (orig.)

  11. Syntheses, crystal structure, and electronic properties of the five ABaMQ4 compounds RbBaPS4, CsBaPS4, CsBaVS4, RbBaVSe4, and CsBaVSe4

    Mesbah, Adel; Prakash, Jai; Rocca, Dario; Lebègue, Sébastien; Beard, Jessica C.; Lewis, Benjamin A.; Ibers, James A.


    Five new compounds belonging to the ABaMQ4 family were synthesized by solid-state chemistry at 1123 K. The compounds RbBaPS4, CsBaPS4, CsBaVS4, RbBaVSe4, and CsBaVSe4 are isostructural and have the TlEuPS4 structure type. They crystallize in space group D162h - Pnma of the orthorhombic system. Their structure consists isolated MQ4 tetrahedra separated by A and Ba atoms to form a salt-like structure. Density Functional Theory (DFT) calculations of the electronic structures with the use of the HSE functional suggest that the compounds are semiconductors with calculated band gaps of 3.3 eV (RbBaPS4), 3.4 eV (CsBaPS4), 2.3 eV (CsBaVS4), and 1.6 eV (RbBaVSe4).

  12. Impact of miR-208 and its Target Gene Nemo-Like Kinase on the Protective Effect of Ginsenoside Rb1 in Hypoxia/Ischemia Injuried Cardiomyocytes

    Xu Yan


    Full Text Available Background/Aims: Ginsenoside Rb1 (GS-Rb1 is one of the most important active pharmacological extracts of the Traditional Chinese Medicine ginseng, with extensive evidence of its cardioprotective properties. Mir-208 has been shown to act as a biomarker of acute myocardial infarction in vivo studies including man. However the impact of miR-208 on the protective effect of GS-Rb1 in hypoxia/ischemia injured cardiomyocytes remains unclear. The current study aims to investigate the target gene of miR-208 and the impact on the protective effect of GS-Rb1 in hypoxia/ischemia (H/I injuried cardiomyocytes. Materials and Methods: Primary cultures of neonatal rat cardiomyocytes (NRCMs was subjected to the H/I conditions with or without GS-Rb1. Cell viability was calculated by MTT assay and confirmed by flow cytometry analysis. Mir-208 was then detected by qRT-PCR. Luciferase reporter assay was carried out to detect the target gene of Mir-208. Then the NRCMs were transfected with miR-208 mimics and inhibitors to evaluate the impact on cardioprotective properties of Rb1. Results: The miR-208 expression level was clearly upregulated in the H/I treated NRCMs accompanied by the percentage of the apoptotic cells which could be reversed by GS-Rb1 pretreatment. The nemo-like kinase (NLK mRNA and protein expression levels were decreased in H/I group measured by RT-PCR and western blotting. Luciferase activity assay was then carried out to identify that NLK may be a direct target of mir-208. MTT assay showed that miR-208 inhibitor slightly decreased the protective effect of Rb1 on the H/I impaired NRCMs. However, results showed no statistical difference. Conclusions: These findings proved that NLK was a direct target of mir-208 and miR-208 act indirectly during Rb1 protecting H/I impaired NRCMs and further researches were needed to explore the relationship that microRNAs and other signal pathways in the protective effect of GS-Rb1 on the hypoxia/ischemia injuries in

  13. The effect of sterol structure on the permeability of lipomes to glucose, glycerol and Rb+

    Demel, R.A.; Bruckdorfer, K.R.; Deenen, L.L.M. van


    1. 1. The effect of 3β-, 3α-hydroxysterol and ketosteroids on the permeability properties of (egg lecithin) liposomes towards glucose, glycerol and Rb+ has been studied. 2. 2. The 3β-hydroxysterols, cholesterol, cholestanol, lathosterol, 7-dehydrocholesterol and B-norcholesterol affect the most pro

  14. Electronic structure and optical properties of RbPb2Br5

    Lavrentyev, A. A.; Gabrelian, B. V.; Vu, V. T.; Denysyuk, N. M.; Shkumat, P. N.; Tarasova, A. Y.; Isaenko, L. I.; Khyzhun, O. Y.


    We report on density functional theory (DFT) calculations of the total and partial densities of states of rubidium dilead pentabromide, RbPb2Br5, employing the augmented plane wave+local orbitals (APW+lo) method as incorporated in the WIEN2k package. The calculations indicate that the Pb 6s and Br 4p states are the dominant contributors to the valence band: their main contributions are found to occur at the bottom and at the top of the band, respectively. Our calculations reveal that the bottom of the conduction band is formed predominantly from contributions of the unoccupied Pb 6p states. Data of total DOS derived in the present DFT calculations are found to be in agreement with the experimental X-ray photoelectron valence-band spectrum of this compound. The predominant contributions of the Br 4p states at the top of the valence band of rubidium dilead pentabromide are confirmed by comparison on a common energy scale of the X-ray emission band representing the energy distribution of the valence Br p states and the X-ray photoelectron valence-band spectrum of the RbPb2Br5 single crystal. Main optical characteristics of RbPb2Br5, such as dispersion of the absorption coefficient, real and imaginary parts of dielectric function, electron energy-loss spectrum, refractive index, extinction coefficient and optical reflectivity are explored for RbPb2Br5 by the DFT calculations.

  15. Data of evolutionary structure change: 1C2RB-1COTA [Confc[Archive

    Full Text Available 1C2RB-1COTA 1C2R 1COT B A -GDAAKGEKEFNKCKTCHSIIAPDGTEIVKGAKTGPNLY...CA 337 THR CA 277 1COT A 37.21200180053711 -25.844999313354492 tion> -0.03099999949336...3 0.597000002861023 tion> 1.6881250143051147 3.115614891052246 ...

  16. 儿童视网膜母细胞瘤患者RB1基因胚系突变的特征分析%Characteristics of RB1 gene mutations in Chinese patients with retinoblastoma

    何明燕; 安宇; 李刚; 钱江; 高怡瑾


    目的 研究国内儿童视网膜母细胞瘤(retinoblastoma,RB)患者RB1胚系突变的特征及其与表型的相关性.方法 收集35例RB患儿的外周静脉血标本,提取白细胞DNA,应用多重PCR测序技术检测其RB1基因的突变情况.收集其中6例RB1突变患儿双亲的外周静脉血标本,研究突变的遗传性.结果 35例RB患者中,共发现14例(40%)患者具有RB1的胚系突变,其中双眼受累11例,单眼受累3例.共检出RB1突变16种,其中13种为致病突变,包括5种无义突变(c.1072C>T、c.1333C>T、c.1363C>T、c.1399C>T、c.2501C>A),4种错义突变(c.920C>T、c.1346G>A、c.1468G>A、c.1861C>A),2种移码突变(c.1947delG、c.2403delA),以及2种大片段缺失突变(c.139_168del30、exon8缺失).3种为非致病性突变,包括2种发生于内含子区的点突变(c.540-23dupT、c.2664-10T>A)和1种同义突变(c.2192T>A).在6例RB1突变患儿双亲的外周血标本中,检出1例患儿母亲携带与患儿相同的突变.结论 对散发的单眼或双眼RB患者进行RB1胚系突变序列分析可以鉴定其是否为遗传型病例,为RB的遗传咨询和临床管理提供依据.%Objective To study the characteristics of RB1 gene mutations in Chinese patients with retinoblastoma.Methods Peripheral blood samples of 35 patients with retinoblastoma were collected and genomic DNA was extracted.Multiplex PCR sequencing was carried out to identify RB1 gene mutations.Parents of 6 probands with RB1 mutations were also enrolled to identify the origins of mutations.Results Fourteen patients were found to have carried germline mutations,among whom 11 had bilateral tumors and 3 had unilateral tumors.Sixteen germline mutations were identified,among which 13 were pathological,which included 5 nonsense mutations (c.1072C>T,c.1333C>T,c.1363C>T,c.1399C>T,c.2501C>A),4 missense mutations (c.920C>T,c.1346G>A,c.1468G>A,c.1861C>A),2 frameshift mutations (c.1947delG,c.2403delA) and 2 large

  17. Immunohistochemical analysis of p53, cyclinD1, RB1, c-fos and N-ras gene expression in hepatocellular carcinoma in Iran

    SJ Moghaddam; EN Haghighi; S Samiee; N Shahid; AR Keramati; S Dadgar; MR Zali


    AIM: To study the effect of some genes especially those involved in cell cycle regulation on hepatocellular carcinoma.METHODS: Paraffin-embedded tissue samples of 25 patients (18 males and 7 females) with hepatocellular carcinoma were collected from 22 pathology centers in Tehran during 2000-2001, and stained using immunohistochemistry method (avidin-biotin-peroxidase)for detection of p53, cyclinD1, RB1, c-fos and N-ras proteins.RESULTS: Six (24%), 5 (20%), 12 (48%) and 2 samples (8%) were positive for p53, cyclinD1, C-fos and N-ras expression, respectively. Twenty-two (88%) samples had alterations in the G1 cell-cycle checkpoint protein expression (RB1 or cyclinD1). P53 positive samples showed a higher (9 times) risk of being positive for RB1 protein than p53 negative samples. Loss of expression of RB1 in association with p53 over-expression was observed in 4 (66.7%) of 6 samples. Loss of expression of RB1 was seen in all cyclinD1 positive, 20 (90.9%) N-ras negative, and 11 (50%) C-fos positive samples,respectively. CyclinD1 positive samples showed a higher (2.85 and 4.75 times) risk of being positive for c-fos and N-ras expression than cyclinD1 negative samples.CONCLUSION: The expression of p53, RB1 and c-fos genes appears to have a key role in the pathogenesis of hepatocellular carcinoma in Iran. Simultaneous overexpression of these genes is significantly associated with their loss of expression during development of hepatocellular carcinoma.

  18. Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.

    Xia, Shuangluo; Wang, Mina; Blaha, Gregor; Konigsberg, William H; Wang, Jimin


    We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-α,β-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the α-phosphorus atom (Pα) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's α-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Pα. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to Pα to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to Pα. This geometric relationship appears to be conserved among DNA polymerases of known structure.

  19. Genes encoding Pir51,Beclin 1,RbAp48 and aldolase b are up or down-regulated in human primary hepatocellular carcinoma

    Hai Song; Shuang-Luo Xia; Cheng Liao; Yi-Liang Li; Yi-Fei Wang; Tsai-Ping Li; Mu-Jun Zhao


    AIM: To reveal new tumor markers and target genes from differentially expressed genes of primary tumor samples using cDNA microarray.METHODS: The 33p labeled cDNAs were synthesized by reverse transcription of message RNA from the liver cancerous tissue and adjacent non-cancerous liver tissue from the same patient and used to hybridize to LifeGrid 1.0cDNA microarray blot containing 8400 known and unique human cDNA gene targets, and an expression profile of genes was produced in one paired human liver tumor tissue.After a global analysis of gene expression of 8400 genes,we selected some genes to confirm the differential expression using Northern blot and RT-PCR.RESULTS: Parallel analysis of the hybridized signals enabled us to get an expression profile of genes in which about 500genes were differentially expressed in the paired liver tumor tissues. We identified 4 genes, the expression of three(Beclin 1, RbAp48 and Pir51) were increased and one (aldolase b)was decreased in liver tumor tissues. In addition, the expression of these genes in 6 hepatoma cell lines was also showed by RT-PCR analysis.CONCLUSION: cDNA microarray permits a high throughput identification of changes in gene expression. The genes encoding Beclin 1, RbAp48, Pir51 and aldolase b are first reported that may be related with hepatocarcinoma.

  20. Synthesis, Crystal Structure, and Nonlinear Optical Properties of a New Alkali and Alkaline Earth Metal Carbonate RbNa5Ca5(CO38

    Qiaoling Chen


    Full Text Available A new nonlinear optical (NLO material, RbNa5Ca5(CO38, has been synthesized by the hydrothermal method. The crystal structure is established by single-crystal X-ray diffraction. RbNa5Ca5(CO38 crystallizes in the hexagonal crystal system with space group P63mc (No. 186. The structure of RbNa5Ca5(CO38 can be described as the adjacent infinite [CaCO3]∞ layers lying in the a-b plane bridged through standing-on-edge [CO3] groups by sharing O atoms (two-fold coordinated to build a framework with four types of tunnels running through the b-axis. The Rb, Na, and [Na0.67Ca0.33] atoms reside in these tunnels, respectively. The measurement of second harmonic generation (SHG indicated that RbNa5Ca5(CO38 is a phase-matchable material, which had SHG responses of approximately 1×KH2PO4 (KDP. Meanwhile, the results from the UV-VIS diffuse reflectance spectroscopy study of the powder samples indicated that the UV cut-off edges of RbNa5Ca5(CO38 is about 203 nm.

  1. Emergence of a few distinct structures from a single formal structure type during high-throughput screening for stable compounds: The case of RbCuS and RbCuSe

    Trimarchi, Giancarlo; Zhang, Xiuwen; DeVries Vermeer, Michael J.; Cantwell, Jacqueline; Poeppelmeier, Kenneth R.; Zunger, Alex


    Theoretical sorting of stable and synthesizable "missing compounds" from those that are unstable is a crucial step in the discovery of previously unknown functional materials. This active research area often involves high-throughput (HT) examination of the total energy of a given compound in a list of candidate formal structure types (FSTs), searching for those with the lowest energy within that list. While it is well appreciated that local relaxation methods based on a fixed list of structure types can lead to inaccurate geometries, this approach is widely used in HT studies because it produces answers faster than global optimization methods (that vary lattice vectors and atomic positions without local restrictions). We find, however, a different failure mode of the HT protocol: specific crystallographic classes of formal structure types each correspond to a series of chemically distinct "daughter structure types" (DSTs) that have the same space group but possess totally different local bonding configurations, including coordination types. Failure to include such DSTs in the fixed list of examined candidate structures used in contemporary high-throughput approaches can lead to qualitative misidentification of the stable bonding pattern, not just quantitative inaccuracies. In this work, we (i) clarify the understanding of the general DST-FST relationship, thus improving current discovery HT approaches, (ii) illustrate this failure mode for RbCuS and RbCuSe (the latter being a yet unreported compound and is predicted here) by developing a synthesis method and accelerated crystal-structure determination, and (iii) apply the genetic-algorithm-based global space-group optimization (GSGO) approach which is not vulnerable to the failure mode of HT searches of fixed lists, demonstrating a correct identification of the stable DST. The broad impact of items (i)-(iii) lies in the demonstrated predictive ability of a more comprehensive search strategy than what is currently

  2. Luminescence and structural properties of RbGdS2 compounds doped by rare earth elements

    Jarý, V.; Havlák, L.; Bárta, J.; Mihóková, E.; Nikl, M.


    Rare earth elements (Pr, Ce) doped ternary sulfides of formula RbGd1-xRExS2 were synthesized in the form of crystalline hexagonal platelets by chemical reaction under the flow of hydrogen sulfide. The X-ray powder diffraction detected only a single crystalline phase of rhombohedral lattice system. Optical properties of studied systems are investigated by methods of time-resolved luminescence spectroscopy. Thermal stability of the Pr3+ emission is demonstrated. Application potential in the white light-emitting diode solid state lighting or X-ray phosphors is discussed.

  3. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations

    Bossini-Castillo, Lara; Martin, Jose-Ezequiel; Broen, Jasper; Gorlova, Olga; Simeón, Carmen P.; Beretta, Lorenzo; Vonk, Madelon C.; Luis Callejas, Jose; Castellví, Ivan; Carreira, Patricia; José García-Hernández, Francisco; Fernández Castro, Mónica; Coenen, Marieke J.H.; Riemekasten, Gabriela; Witte, Torsten; Hunzelmann, Nicolas; Kreuter, Alexander; Distler, Jörg H.W.; Koeleman, Bobby P.; Voskuyl, Alexandre E.; Schuerwegh, Annemie J.; Palm, Øyvind; Hesselstrand, Roger; Nordin, Annika; Airó, Paolo; Lunardi, Claudio; Scorza, Raffaella; Shiels, Paul; van Laar, Jacob M.; Herrick, Ariane; Worthington, Jane; Denton, Christopher; Tan, Filemon K.; Arnett, Frank C.; Agarwal, Sandeep K.; Assassi, Shervin; Fonseca, Carmen; Mayes, Maureen D.; Radstake, Timothy R.D.J.; Martin, Javier


    A single-nucleotide polymorphism (SNP) at the IL12RB2 locus showed a suggestive association signal in a previously published genome-wide association study (GWAS) in systemic sclerosis (SSc). Aiming to reveal the possible implication of the IL12RB2 gene in SSc, we conducted a follow-up study of this locus in different Caucasian cohorts. We analyzed 10 GWAS-genotyped SNPs in the IL12RB2 region (2309 SSc patients and 5161 controls). We then selected three SNPs (rs3790567, rs3790566 and rs924080) based on their significance level in the GWAS, for follow-up in an independent European cohort comprising 3344 SSc and 3848 controls. The most-associated SNP (rs3790567) was further tested in an independent cohort comprising 597 SSc patients and 1139 controls from the USA. After conditional logistic regression analysis of the GWAS data, we selected rs3790567 [PMH= 1.92 × 10−5 odds ratio (OR) = 1.19] as the genetic variant with the firmest independent association observed in the analyzed GWAS peak of association. After the first follow-up phase, only the association of rs3790567 was consistent (PMH= 4.84 × 10−3 OR = 1.12). The second follow-up phase confirmed this finding (Pχ2 = 2.82 × 10−4 OR = 1.34). After performing overall pooled-analysis of all the cohorts included in the present study, the association found for the rs3790567 SNP in the IL12RB2 gene region reached GWAS-level significant association (PMH= 2.82 × 10−9 OR = 1.17). Our data clearly support the IL12RB2 genetic association with SSc, and suggest a relevant role of the interleukin 12 signaling pathway in SSc pathogenesis. PMID:22076442

  4. Crystal Structure and Topological Aspects of the High-Temperature Phases of the Alkali-metal Oxalates M-2 C2O4(M= K,Rb, Cs)

    Dinnebier,R.; Vensky, S.; Jensen, M.; Hanson, J.


    The high-temperature phases of the alkali-metal oxalates M{sub 2}[C{sub 2}O{sub 4}] (M=K, Rb, Cs), and their decomposition products M{sub 2}[CO{sub 3}] (M=K, Rb, Cs), were investigated by fast, angle-dispersive X-ray powder diffraction with an image-plate detector, and also by simultaneous differential thermal analysis (DTA)/thermogravimetric analysis (TGA)/mass spectrometry (MS) and differential scanning calorimetry (DSC) techniques. The following phases, in order of decreasing temperature, were observed and crystallographically characterized (an asterisk denotes a previously unknown modification): *{alpha}-K{sub 2}[C{sub 2}O{sub 4}], *{alpha}-Rb{sub 2}[C{sub 2}O{sub 4}], *{alpha}-Cs{sub 2}[C{sub 2}O{sub 4}], {alpha}-K{sub 2}[CO{sub 3}], *{alpha}-Rb{sub 2}[CO{sub 3}], and *{alpha}-Cs{sub 2}[CO{sub 3}] in space group P6{sub 3}/mmc; *{beta}-Rb{sub 2}[C{sub 2}O{sub 4}], *{beta}-Cs{sub 2}[C{sub 2}O{sub 4}], *{beta}-Rb{sub 2}[CO{sub 3}], and *{beta}-Cs{sub 2}[CO{sub 3}] in Pnma; {gamma}-Rb{sub 2}[C{sub 2}O{sub 4}], {gamma}-Cs[C{sub 2}O{sub 4}], {gamma}-Rb{sub 2}[CO{sub 3}], and {gamma}-Cs{sub 2}[CO{sub 3}] in P2{sub 1}/c; and {delta}-K{sub 2}[C{sub 2}O{sub 4}] and {delta}-Rb{sub 2}[C{sub 2}O{sub 4}] in Pbam. With respect to the centers of gravity of the oxalate and carbonate anions, respectively, the crystal structures of all known alkali-metal oxalates and carbonates belong to the AlB{sub 2} family, and adopt either the AlB{sub 2} or the Ni{sub 2}In arrangement depending on the size of the cation and the temperature. Despite the different sizes and constitutions of the carbonate and oxalate anions, the high-temperature phases of the alkali-metal carbonates M{sub 2}[CO{sub 3}] (M=K, Rb, Cs), exhibit the same sequence of basic structures as the corresponding alkali-metal oxalates. The topological aspects and order-disorder phenomena at elevated temperature are discussed.

  5. The histone demethylase Jarid1b (Kdm5b is a novel component of the Rb pathway and associates with E2f-target genes in MEFs during senescence.

    Jeroen H Nijwening

    Full Text Available Senescence is a robust cell cycle arrest controlled by the p53 and Rb pathways that acts as an important barrier to tumorigenesis. Senescence is associated with profound alterations in gene expression, including stable suppression of E2f-target genes by heterochromatin formation. Some of these changes in chromatin composition are orchestrated by Rb. In complex with E2f, Rb recruits chromatin modifying enzymes to E2f target genes, leading to their transcriptional repression. To identify novel chromatin remodeling enzymes that specifically function in the Rb pathway, we used a functional genetic screening model for bypass of senescence in murine cells. We identified the H3K4-demethylase Jarid1b as novel component of the Rb pathway in this screening model. We find that depletion of Jarid1b phenocopies knockdown of Rb1 and that Jarid1b associates with E2f-target genes during cellular senescence. These results suggest a role for Jarid1b in Rb-mediated repression of cell cycle genes during senescence.

  6. Structural plasticity of histones H3-H4 facilitates their allosteric exchange between RbAp48 and ASF1.

    Zhang, Wei; Tyl, Marek; Ward, Richard; Sobott, Frank; Maman, Joseph; Murthy, Andal S; Watson, Aleksandra A; Fedorov, Oleg; Bowman, Andrew; Owen-Hughes, Tom; El Mkami, Hassane; Murzina, Natalia V; Norman, David G; Laue, Ernest D


    The mechanisms by which histones are disassembled and reassembled into nucleosomes and chromatin structure during DNA replication, repair and transcription are poorly understood. A better understanding of the processes involved is, however, crucial if we are to understand whether and how histone variants and post-translationally modified histones are inherited in an epigenetic manner. To this end we have studied the interaction of the histone H3-H4 complex with the human retinoblastoma-associated protein RbAp48 and their exchange with a second histone chaperone, anti-silencing function protein 1 (ASF1). Exchange of histones H3-H4 between these two histone chaperones has a central role in the assembly of new nucleosomes, and we show here that the H3-H4 complex has an unexpected structural plasticity, which is important for this exchange.

  7. Expression of the lncRNA Maternally Expressed Gene 3 (MEG3) Contributes to the Control of Lung Cancer Cell Proliferation by the Rb Pathway


    Maternally expressed gene 3 (MEG3, mouse homolog Gtl2) encodes a long noncoding RNA (lncRNA) that is expressed in many normal tissues, but is suppressed in various cancer cell lines and tumors, suggesting it plays a functional role as a tumor suppressor. Hypermethylation has been shown to contribute to this loss of expression. We now demonstrate that MEG3 expression is regulated by the retinoblastoma protein (Rb) pathway and correlates with a change in cell proliferation. Microarray analysis ...

  8. RB975242 and RB975201 - Late maturation sugarcane varieties

    Monalisa Sampaio Carneiro


    Full Text Available The sugarcane varieties RB975201 and RB975242 were developed and released for harvest at the end of the season (late maturation in the CentralSouth region of Brazil. In specific environments, these varieties were compared with commercial standards in sugar yield per area. They are resistant to major sugarcane diseases and present the Bru1 gene of resistance to brown rust.

  9. Rb, Sr and strontium isotopic composition, K/Ar age and large ion lithophile trace element abundances in rocks and glasses from the Wanapitei Lake impact structure

    Winzer, S. R.; Lum, R. K. L.; Schuhmann, S.


    Shock metamorphosed rocks and shock-produced melt glasses from the Wanapitei Lake impact structure have been examined petrographically and by electron microprobe. Eleven clasts exhibiting varying degrees of shock metamorphism and eight impact-produced glasses have been analyzed for Rb, Sr and Sr isotopic composition. Five clasts and one glass have also been analyzed for large ion lithophile (LIL) trace element abundances including Li, Rb, Sr, and Ba and the REE's. The impact event forming the Wanapitei Lake structure occurred 37 m.y. ago based on K/Ar dating of glass and glassy whole-rock samples. Rb/Sr isotopic dating failed to provide a meaningful whole-rock or internal isochron. The isotopic composition of the glasses can be explained by impact-produced mixing and melting of metasediments.

  10. A3V5O14 (A = K+, Rb+, or Tl+), new polar oxides with a tetragonal tungsten bronze related structural topology: synthesis, structure, and functional properties.

    Yeon, Jeongho; Kim, Sang-Hwan; Halasyamani, P Shiv


    Three polar noncentrosymmetric (NCS) oxide materials, A(3)V(5)O(14) (A = K(+), Rb(+), or Tl(+)), have been synthesized by hydrothermal and conventional solid state techniques. Their crystal structures and functional properties (second-harmonic generation, piezoelectricity, and polarization) have been determined. The iso-structural materials exhibit a layered structural topology that consists of corner-sharing VO(4) tetrahedra and VO(5) square pyramids. The layers stack parallel to the c-axis direction and are separated by the K(+), Rb(+), or Tl(+) cations. Powder second-harmonic generation (SHG) measurements using 1064 nm radiation indicate the materials exhibit moderate SHG efficiencies of approximately 100 x alpha-SiO(2). Additional SHG measurements, that is, particle size versus SHG efficiency, indicate the materials are type-I phase-matchable. Converse piezoelectric measurements for K(3)V(5)O(14), Rb(3)V(5)O(14), and Tl(3)V(5)O(14) revealed d(33) values of 28, 22, and 26 pm/V, respectively. Pyroelectric measurements, that is, temperature-dependent polarization measurements, resulted in pyroelectric coefficients of -2.2, -2.9, and -2.8 microC/m(2) x K at 65 degrees C, for K(3)V(5)O(14), Rb(3)V(5)O(14), and Tl(3)V(5)O(14) respectively. Frequency-dependent polarization measurements confirmed that all of the materials are nonferroelectric, consistent with our first principle density functional theory (DFT) electronic structure calculations. Infrared, UV-vis, thermogravimetric, and differential scanning calorimetry measurements were also performed. Crystal data: K(3)V(5)O(14), trigonal, space group P31m (No. 157), a = 8.6970(16) A, c = 4.9434(19) A, V = 323.81(15), and Z = 1; Rb(3)V(5)O(14), trigonal, space group P31m (No. 157), a = 8.7092(5) A, c = 5.2772(7) A, V = 346.65(5), and Z = 1; Tl(3)V(5)O(14), trigonal, space group P31m (No. 157), a = 8.7397(8) A, c = 5.0846(10) A, V = 336.34(8), and Z = 1.

  11. Synthesis and structure of (Rb0.50Ba0.25)[UO2(CH3COO)3

    Serezhkina, L. B.; Peresypkina, E. V.; Virovets, A. V.; Klepov, V. V.


    A new compound (Rb0.50Ba0.25)[UO2(CH3COO)3] is synthesized and its crystal structure is studied by X-ray diffraction. The compound crystallizes in the form of yellow plates belonging to the cubic crystal system. The unit cell parameter a = 17.0367(1) Å, V = 4944.89(5) Å3, space group I bar 4 3 d, Z = 16, and R = 0.0182. The coordination polyhedron of the uranium atom is a hexagonal bipyramid with oxygen atoms of three acetate groups and the uranyl group in the vertices. The crystal chemical formula of the uranium-containing group is AB {3/01}( A = UO{2/2+}, B 01 = CH3COO-). The oxygen atoms of the acetate groups that enter the coordination polyhedron of uranium are bound to barium and rubidium atoms.

  12. Level structure of 82Rb, studied through the 81Br(α, 3n) reaction

    Behar, M.; Filevich, A.; Bermudez, G. García; Mariscotti, M. A. J.; Szybisz, L.


    Nuclear states of 82Rb were studied through the 81Br(α, 3n) reaction at various bombarding energies between 30 and 55 MeV. Excitation functions, γ-ray angular distributions, γ-γ coincidences and γ-time distributions with respect to the beam bursts were determined. Levels at 123.2, 187.7, 233.6, 796.3, 1214.1 keV and tentatively at 1835.5 keV were observed. It was not possible to establish whether the lowest state of the proposed level scheme corresponds to the ground state or to the T {1}/{2} = 6.2 h isomeric state. The 45.9 and 64.5 keV γ-rays do not exhibit any measurable lifetime and a limit T {1}/{2} ≦ 5 ns has been determined. The situation is similar for the 123.2 keV γ-ray, although in this case the presence of a long-lived component cannot be ruled out.

  13. RNAi mediated acute depletion of Retinoblastoma protein (pRb promotes aneuploidy in human primary cells via micronuclei formation

    Iovino Flora


    Full Text Available Abstract Background Changes in chromosome number or structure as well as supernumerary centrosomes and multipolar mitoses are commonly observed in human tumors. Thus, centrosome amplification and mitotic checkpoint dysfunctions are believed possible causes of chromosomal instability. The Retinoblastoma tumor suppressor (RB participates in the regulation of synchrony between DNA synthesis and centrosome duplication and it is involved in transcription regulation of some mitotic genes. Primary human fibroblasts were transfected transiently with short interfering RNA (siRNA specific for human pRb to investigate the effects of pRb acute loss on chromosomal stability. Results Acutely pRb-depleted fibroblasts showed altered expression of genes necessary for cell cycle progression, centrosome homeostasis, kinetochore and mitotic checkpoint proteins. Despite altered expression of genes involved in the Spindle Assembly Checkpoint (SAC the checkpoint seemed to function properly in pRb-depleted fibroblasts. In particular AURORA-A and PLK1 overexpression suggested that these two genes might have a role in the observed genomic instability. However, when they were post-transcriptionally silenced in pRb-depleted fibroblasts we did not observe reduction in the number of aneuploid cells. This finding suggests that overexpression of these two genes did not contribute to genomic instability triggered by RB acute loss although it affected cell proliferation. Acutely pRb-depleted human fibroblasts showed the presence of micronuclei containing whole chromosomes besides the presence of supernumerary centrosomes and aneuploidy. Conclusion Here we show for the first time that RB acute loss triggers centrosome amplification and aneuploidy in human primary fibroblasts. Altogether, our results suggest that pRb-depleted primary human fibroblasts possess an intact spindle checkpoint and that micronuclei, likely caused by mis-attached kinetochores that in turn trigger

  14. Ion mobility, conductivity, structure, and phase transitions in K0.7M0.3SbF4 compounds with M=Rb, NH4

    Kavun, V. Ya.; Gerasimenko, A. V.; Uvarov, N. F.; Polyantsev, M. M.; Zemnukhova, L. A.


    Ion mobility, phase transitions, structure, and conductivity in the K0.7M0.3SbF4 (M=Rb, NH4) compounds were studied by NMR spectroscopy, DSC, X-ray, and conductivity measurements. The predominant form in the ion motions resulting from the phase transition of high modification was diffusion of fluoride and ammonium ions above 450 K. The high-temperature phases of K0.7M0.3SbF4 (M=Rb, NH4) are superionic, while their conductivity attains the values of ~10-2-10-4 S/cm at 450-500 K. The structures of α- and β-modifications of the K0.7Rb0.3SbF4 are monoclinic (space group P21/m). The main structural units in them are statistically substituting each other K+ and Rb+ cations and complex 1[ SbF4 ]- ∞ anions linked into zigzag-like chains by bridge fluorine atoms. The nearest surrounding of each antimony atom contains five fluorine atoms, so that the antimony coordination polyhedron can be described, taking into account the lone electron pair, as a distorted SbF5E octahedron (ψ-octahedron).


    Eny Ida Riyanti


    Full Text Available Late blight caused by Phytophthora infestans is an important disease on potato.  Several potato hybrids have been generated by crossing local varieties (Atlantic and Granola with Katahdin SP951 which contains late blight resistance gene RB.  Prior to release, these hybrids need to be evaluated for their environ-mental effects on non-target organisms and natural pests and diseases. The objectives of the study were to investigate the effect of LBR potato hybrids on beneficial soil microbes, pests and diseases. The trial was conducted in the confined field trial (CFT in Lembang, West Java. The parental non-transgenic (NT clones (Granola, Atlantic and Katahdin and LBR hybrids (four clones of Atlantic x Katahdin SP951 hybrids; 10 clones of Granola x Katahdin SP951 were planted at a plant spacing of 30 cm x 70 cm. Fungicide applications were used as treat-ments (no spray, five and twenty times sprays. The experi-ment was arranged in a randomized completely block design with three replications. The parameters determined were popula-tions of N2 fixing and P solubilizing bacteria, soil C/N ratio as well as natural pests and diseases. The results showed that the transgenic LBR potato hybrids did not have negative effect on N fixing bacteria. The bacterial populations were around 1010-11 cells g-1 soil before planting, 1012 cells at 1.5 months after planting (MAP and 108 cells after harvest. For P- solubilizing bacteria, their populations were 1010 cells before planting, 1012 cells at 1.5 MAP and 1011 cells g-1  soil after harvest. The soil C/N ratio of the transgenic plot was not statistically different compared to non-transgenic plot, i.e. 12-15 before planting, 10-11 at 1.5 MAP, and 10 after harvest in non-spray plot. Pests and diseases such as Alternaria solani, Liriomyza, potato tubber moth, aphid and mites on the transgenic and non-transgenic plots were statistically not different. The resistance score for A. solani was 7.2 (parental tansgenic and

  16. RB1: a prototype tumor suppressor and an enigma.

    Dyson, Nicholas J


    The retinoblastoma susceptibility gene (RB1) was the first tumor suppressor gene to be molecularly defined. RB1 mutations occur in almost all familial and sporadic forms of retinoblastoma, and this gene is mutated at variable frequencies in a variety of other human cancers. Because of its early discovery, the recessive nature of RB1 mutations, and its frequency of inactivation, RB1 is often described as a prototype for the class of tumor suppressor genes. Its gene product (pRB) regulates transcription and is a negative regulator of cell proliferation. Although these general features are well established, a precise description of pRB's mechanism of action has remained elusive. Indeed, in many regards, pRB remains an enigma. This review summarizes some recent developments in pRB research and focuses on progress toward answers for the three fundamental questions that sit at the heart of the pRB literature: What does pRB do? How does the inactivation of RB change the cell? How can our knowledge of RB function be exploited to provide better treatment for cancer patients?

  17. Synthesis and single-crystal structure of the pseudo-ternary compounds LiA[N(CN){sub 2}]{sub 2} (A = K or Rb)

    Reckeweg, Olaf; DiSalvo, Francis J. [Cornell Univ., Ithaca, NY (United States). Baker Lab.


    Crystals of LiA[N(CN){sub 2}]{sub 2} were obtained from the reaction of LiCl and ACl (A = K or Rb) with Ag[N(CN){sub 2}] in water and subsequent evaporation of the filtered solution at 80 C under normal atmospheric conditions. Crystals of the title compound form thin rectangular plates that are transparent, colorless, and very fragile. Single-crystal structure analyses have shown that both compounds are isotypic and adopt the tetragonal space group I4/mcm (no. 140, Z = 4) with the cell parameters a = 701.53(12) and c = 1413.7(5) pm for LiK[N(CN){sub 2}]{sub 2} and a = 730.34(10) and c = 1414.4(4) pm for LiRb[N(CN){sub 2}]{sub 2}. The crystal structure is described and compared to that of the pseudo-binary alkali metal dicyanamides.

  18. Crystal and molecular structure of rubidium peroxodicarbonate Rb2[C2O6].

    Dinnebier, Robert E; Vensky, Sascha; Jansen, Martin


    We report the crystal structure of rubidium peroxodicarbonate, which was synthesized by electrocrystallization at T=257 K, from laboratory X-ray powder diffraction data. The compound crystallizes in the monoclinic space group P2(1)/c with four formula units per unit cell and cell parameters of a=7.9129(1), b=10.5117(1), c=7.5559(1) A, beta=102.001(1) degrees, and V=614.75(1) A(3). The packing can be considered as a strongly distorted CsCl type of structure. The conformation of the peroxodicarbonate anion was found to be planar (C(2h) symmetry), in contrast to the staggered conformation of the peroxodicarbonate anion in the respective potassium peroxodicarbonate. The different conformation is attributed to packing effects.

  19. Crystal Structure and Ionic Conductivity of Three Polymorphic Phases of Rubidium Trefluoromethyl Sulfonate, RbSO3CF3

    Hildebrandt,L.; Dinnebier, R.; Jansen, M.


    The crystal structures of three polymorphic phases of rubidium trifluoromethyl sulfonate (RbSO{sub 3}CF{sub 3}, rubidium 'triflate') were solved from X-ray powder diffraction data. At room temperature, rubidium triflate crystallizes in the monoclinic space group Cm with lattice parameters of a = 19.9611(5) Angstroms, b = 23.4913(7) Angstroms, c = 5.1514(2) Angstroms, = 102.758(2); Z = 16. At T = 321 K, a first-order phase transition occurs toward a monoclinic phase in space group P2{sub 1} with lattice parameters at T = 344 K of a = 10.3434(5) Angstroms, b = 5.8283(3) Angstroms, c = 5.1982(3) Angstroms, = 104.278(6); Z = (2). At T = 461 K, another phase transition, this time of second order, occurs toward an orthorhombic phase in space group Cmcm with lattice parameters at T = 510 K of a = 5.3069(2) Angstroms, b = 20.2423(10) Angstroms, c = 5.9479(2) Angstroms; Z = 4. As a common feature within all three crystal structures of rubidium triflate, the triflate anions are arranged in double layers with the lipophilic CF{sub 3} groups facing each other. The rubidium ions are located between the SO{sub 3} groups. The general packing is similar to the packing in cesium triflate. Rubidium triflate can be classified as a solid electrolyte with a specific ionic conductivity of = 9.89 x 10{sup -9} S/cm at T = 384 K and = 3.84 x 10{sup -6} S/cm at T = 481 K.

  20. Crystal structure and ionic conductivity of three polymorphic phases of rubidium trifluoromethyl sulfonate, RbSO3CF3.

    Hildebrandt, Lars; Dinnebier, Robert; Jansen, Martin


    The crystal structures of three polymorphic phases of rubidium trifluoromethyl sulfonate (RbSO3CF3, rubidium 'triflate') were solved from X-ray powder diffraction data. At room temperature, rubidium triflate crystallizes in the monoclinic space group Cm with lattice parameters of a = 19.9611(5) A, b = 23.4913(7) A, c = 5.1514(2) A, beta = 102.758(2) degrees; Z = 16. At T = 321 K, a first-order phase transition occurs toward a monoclinic phase in space group P2(1) with lattice parameters at T = 344 K of a = 10.3434(5) A, b = 5.8283(3) A, c = 5.1982(3) A, beta = 104.278(6) degrees; Z = 2). At T = 461 K, another phase transition, this time of second order, occurs toward an orthorhombic phase in space group Cmcm with lattice parameters at T = 510 K of a = 5.3069(2) A, b = 20.2423(10) A, c = 5.9479(2) A; Z = 4. As a common feature within all three crystal structures of rubidium triflate, the triflate anions are arranged in double layers with the lipophilic CF3 groups facing each other. The rubidium ions are located between the SO3 groups. The general packing is similar to the packing in cesium triflate. Rubidium triflate can be classified as a solid electrolyte with a specific ionic conductivity of sigma = 9.89 x 10(-9) S/cm at T = 384 K and sigma = 3.84 x 10(-6) S/cm at T = 481 K.

  1. Identification of the genomic mutation in Epha4(rb-2J/rb-2J) mice.

    Mohd-Zin, Siti W; Abdullah, Nor-Linda; Abdullah, Aminah; Greene, Nicholas D E; Cheah, Pike-See; Ling, King-Hwa; Yusof, Hadri; Marwan, Ahmed I; Williams, Sarah M; York, Kerri T; Ahmad-Annuar, Azlina; Abdul-Aziz, Noraishah M


    The EphA4 receptor tyrosine kinase is involved in numerous cell-signalling activities during embryonic development. EphA4 has the ability to bind to both types of ephrin ligands, the ephrinAs and ephrinBs. The C57BL/6J-Epha4rb-2J/GrsrJ strain, denoted Epha4(rb-2J/rb-2J), is a spontaneous mouse mutant that arose at The Jackson Laboratory. These mutants exhibited a synchronous hind limb locomotion defect or "hopping gait" phenotype, which is also characteristic of EphA4 null mice. Genetic complementation experiments suggested that Epha4(rb-2J) corresponds to an allele of EphA4, but details of the genomic defect in this mouse mutant are currently unavailable. We found a single base-pair deletion in exon 9 resulting in a frame shift mutation that subsequently resulted in a premature stop codon. Analysis of the predicted structure of the truncated protein suggests that both the kinase and sterile α motif (SAM) domains are absent. Definitive determination of genotype is needed for experimental studies of mice carrying the Epha4(rb-2J) allele, and we have also developed a method to ease detection of the mutation through RFLP. Eph-ephrin family members are reportedly expressed as numerous isoforms. Hence, delineation of the specific mutation in EphA4 in this strain is important for further functional studies, such as protein-protein interactions, immunostaining and gene compensatory studies, investigating the mechanism underlying the effects of altered function of Eph family of receptor tyrosine kinases on phenotype.

  2. Synthesis and Structural Characterization of the New Clathrates K8Cd4Ge42, Rb8Cd4Ge42, and Cs8Cd4Ge42

    Marion C. Schäfer


    Full Text Available This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K8Cd3.77(7Ge42.23, Rb8Cd3.65(7Ge42.35, and Cs7.80(1Cd3.65(6Ge42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. This and several other details of the crystal chemistry are elaborated.

  3. Structural, electronic and elastic properties of KCaF{sub 3} and RbCaF{sub 3} for vacuum-ultraviolet-transparent lens materials

    Babu, K. Ephraim; Murali, N.; Babu, K. Vijaya; Veeraiah, V., E-mail: [Modelling and Simulation in Materials Science Laboratory, Department of Physics, Andhra University, Visakhapatnam-530 003 (India); Babu, B. Kishore [Department of Engineering Chemistry, AUCE(A), Andhra University, Visakhapatnam-530003 (India)


    The first principles calculation within the full potential linearized augmented plane wave (FP-LAPW) method is applied to study the structural, electronic and elastic properties of cubic perovskite-type compounds KCaF{sub 3} and RbCaF{sub 3}. The exchange correlation effects are included through the LDA, GGA and modified Becke-Johnson (mBJ) exchange potential. The calculated structural properties such as equilibrium lattice constant, the bulk modulus and its pressure derivative are in good agreement with the available data. KCaF{sub 3} and RbCaF{sub 3} have wide and indirect band gaps and they agree with experimental values. The elastic properties such as elastic constants, anisotropy factor, shear modulus, Young’s modulus and Poisson’s ratio are obtained for the first time. KCaF{sub 3} and RbCaF{sub 3} are elastically anisotropic and the B/G ratio indicate that these are ductile materials.

  4. The multiple connections between pRB and cell metabolism.

    Nicolay, Brandon N; Dyson, Nicholas J


    The pRB tumor suppressor is traditionally seen as an important regulator of the cell cycle. pRB represses the transcriptional activation of a diverse set of genes by the E2F transcription factors and prevents inappropriate S-phase entry. Advances in our understanding of pRB have documented roles that extend beyond the cell cycle and this review summarizes recent studies that link pRB to the control of cell metabolism. pRB has been shown to regulate glucose tolerance, mitogenesis, glutathione synthesis, and the expression of genes involved in central carbon metabolism. Several studies have demonstrated that pRB directly targets a set of genes that are crucial for nucleotide metabolism, and this seems likely to represent one of the ways by which pRB influences the G1/S-phase transition and S-phase progression.

  5. Synthesis and structural characterization of a new rubidium borosulfate, Rb{sub 5}BS{sub 4}O{sub 16}

    Dong, Lingyun [Key Laboratory of Functional Materials and Devices for Special Environments of CAS, Xinjiang Technical Institute of Physics and Chemistry of CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi 830011 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Pan, Shilie, E-mail: [Key Laboratory of Functional Materials and Devices for Special Environments of CAS, Xinjiang Technical Institute of Physics and Chemistry of CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi 830011 (China); Wang, Ying; Yu, Hongwei; Lin, Xiaoxia [Key Laboratory of Functional Materials and Devices for Special Environments of CAS, Xinjiang Technical Institute of Physics and Chemistry of CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi 830011 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Han, Shujuan [Key Laboratory of Functional Materials and Devices for Special Environments of CAS, Xinjiang Technical Institute of Physics and Chemistry of CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi 830011 (China)


    Highlights: • Rb{sub 5}BS{sub 4}O{sub 16} has been synthesized using (NH{sub 4}){sub 2}SO{sub 4} as a source of sulfate ions for the first time. • Zero-dimensional anion groups, [B(SO{sub 4}){sub 4}]{sup 5−}, exist in the title compound. • Spectral properties and thermal analysis of Rb{sub 5}BS{sub 4}O{sub 16} were reported. - Abstract: A new rubidium borosulfate, Rb{sub 5}BS{sub 4}O{sub 16}, has been synthesized using (NH{sub 4}){sub 2}SO{sub 4} as a source of sulfate ions for the first time. The compound crystallizes in the space group P4{sub 3}2{sub 1}2 (No. 96) of the tetragonal system with a = 10.148(4) Å, c = 16.689(14) Å, V = 1718.8(17) Å{sup 3}, and Z = 4. Zero-dimensional anion groups, [B(SO{sub 4}){sub 4}]{sup 5−}, a central BO{sub 4} tetrahedron sharing all its four vertices with neighboring sulfate tetrahedra, exist in the title compound, and then the rubidium atoms are situated in the voids of the resulting structure. The IR spectrum confirms the presence of BO{sub 4} and SO{sub 4} units. The UV–vis-NIR diffuse reflectance spectrum exhibits a band gap of about 3.99 eV. The TG-DSC analysis suggests that Rb{sub 5}BS{sub 4}O{sub 16} is an incongruent melting compound.

  6. Discovery of a Red-Emitting Li3RbGe8O18:Mn(4+) Phosphor in the Alkali-Germanate System: Structural Determination and Electronic Calculations.

    Singh, Satendra Pal; Kim, Minseuk; Park, Woon Bae; Lee, Jin-Woong; Sohn, Kee-Sun


    A solid-state combinatorial chemistry approach, which used the A-Ge-O (A = Li, K, Rb) system doped with a small amount of Mn(4+) as an activator, was adopted in a search for novel red-emitting phosphors. The A site may have been composed of either a single alkali metal ion or of a combination of them. This approach led to the discovery of a novel phosphor in the above system with the chemical formula Li3RbGe8O18:Mn(4+). The crystal structure of this novel phosphor was solved via direct methods, and subsequent Rietveld refinement revealed a trigonal structure in the P3̅1m space group. The discovered phosphor is believed to be novel in the sense that neither the crystal structure nor the chemical formula matches any of the prototype structures available in the crystallographic information database (ICDD or ICSD). The measured photoluminescence intensity that peaked at a wavelength of 667 nm was found to be much higher than the best intensity obtained among all the existing A2Ge4O9 (A = Li, K, Rb) compounds in the alkali-germanate system. An ab initio calculation based on density function theory (DFT) was conducted to verify the crystal structure model and compare the calculated value of the optical band gap with the experimental results. The optical band gap obtained from diffuse reflectance measurement (5.26 eV) and DFT calculation (4.64 eV) results were in very good agreement. The emission wavelength of this phosphor that exists in the deep red region of the electromagnetic spectrum may be very useful for increasing the color gamut of LED-based display devices such as ultrahigh-definition television (UHDTV) as per the ITU-R BT.2020-2 recommendations and also for down-converter phosphors that are used in solar-cell applications.

  7. RB1 mutation spectrum in a comprehensive nationwide cohort of retinoblastoma patients

    Dommering, Charlotte J.; Mol, Berber M.; Moll, Annette C.; Burton, Margaret; Cloos, Jacqueline; Dorsman, Josephine C.; Meijers-Heijboer, Hanne; van der Hout, Annemarie H.


    Background Retinoblastoma (Rb) is a childhood cancer of the retina, commonly initiated by biallelic inactivation of the RB1 gene. Knowledge of the presence of a heritable RB1 mutation can help in risk management and reproductive decision making. We report here on RB1 mutation scanning in a unique na

  8. Growth, structural, spectral, mechanical and dielectric characterization of RbCl-doped L-alanine hydrogen chloride monohydrate single crystals

    Lucia Rose, A. S. J.; Selvarajan, P.; Perumal, S.


    Pure (undoped) and RbCl-doped LAHC single crystals were grown successfully by the solution method with the slow evaporation technique at room temperature. The grown crystals were colourless and transparent. The solubility of the grown samples were found out at various temperatures. The lattice parameters of the grown crystals were determined by the single crystal X-ray diffraction technique and the diffracting planes were indentified by recording the powder X-ray diffraction pattern. UV-visible transmittance studies were carried out for the grown samples. Chemical analysis and atomic absorption studies indicate the presence of rubidium in the doped LAHC crystals. Nonlinear optical studies reveal that the SHG efficiency increases when the LAHC crystal is doped with rubidium chloride (RbCl). From microhardness studies, it is observed that the RbCl-doped LAHC crystal is harder than the pure sample. It is observed that the dielectric properties of the LAHC crystal are altered when it is doped with rubidium chloride.

  9. Skin tumors Rb(eing uncovered



    Full Text Available The Rb1 gene was the first bona fide tumor suppressor identified and cloned more than 25 years ago. Since then, a plethora of studies have revealed the functions of pRb and the existence of a sophisticated and strictly regulated pathway that modulates such functional roles. An emerging paradox affecting Rb1 in cancer connects the relatively low number of mutations affecting Rb1 gene in specific human tumors, compared with the widely functional inactivation of pRb in most, if not in all, human cancers. The existence of a retinoblastoma family of proteins pRb, p107 and p130 and their potential unique and overlapping functions as master regulators of cell cycle progression and transcriptional modulation by similar processes, may provide potential clues to explain such conundrum. Here, we will review the development of different genetically engineered mouse models, in particular those affecting stratified epithelia, and how they have offered new avenues to understand the roles of the Rb family members and their targets in the context of tumor development and progression.

  10. Electronic structure in a one-Fe Brillouin zone of the iron pnictide superconductors CsFe2As2 and RbFe2As2

    Kong, S.; Liu, D. Y.; Cui, S. T.; Ju, S. L.; Wang, A. F.; Luo, X. G.; Zou, L. J.; Chen, X. H.; Zhang, G. B.; Sun, Z.


    Using angle-resolved photoemission spectroscopy, we studied the electronic structures of CsFe2As2 and RbFe2As2 . Contrary to other iron-based superconductors where the band structures are usually depicted in the two-Fe Brillouin zone (BZ), we found that the distribution of electronic spectral weight in CsFe2As2 and RbFe2As2 follows the one-Fe BZ, and that the emerging band structure is qualitatively consistent with theoretical band calculations of the one-Fe BZ except for some shadow band effect. Our data suggest that the interlayer separation is an important tuning factor for the physics of FeAs layers, the increase of which can reduce the coupling between Fe and As and lead to the emergence of the electronic structure in accord with the one-Fe symmetry of the Fe square lattice. Our finding puts strong constraints on the theoretical models constructed on the basis of the one-Fe BZ.

  11. Crystal structures and hydrogen bonding in the isotypic series of hydrated alkali metal (K, Rb and Cs complexes with 4-aminophenylarsonic acid

    Graham Smith


    Full Text Available The structures of the alkali metal (K, Rb and Cs complex salts with 4-aminophenylarsonic acid (p-arsanilic acid manifest an isotypic series with the general formula [M2(C6H7AsNO32(H2O3], with M = K {poly[di-μ3-4-aminophenylarsonato-tri-μ2-aqua-dipotassium], [K2(C6H7AsNO32(H2O3], (I}, Rb {poly[di-μ3-4-aminophenylarsonato-tri-μ2-aqua-dirubidium], [Rb2(C6H7AsNO32(H2O3], (II}, and Cs {poly[di-μ3-4-aminophenylarsonato-tri-μ2-aqua-dirubidium], [Cs2(C6H7AsNO32(H2O3], (III}, in which the repeating structural units lie across crystallographic mirror planes containing two independent and different metal cations and a bridging water molecule, with the two hydrogen p-arsanilate ligands and the second water molecule lying outside the mirror plane. The bonding about the two metal cations in all complexes is similar, one five-coordinate, the other progressing from five-coordinate in (I to eight-coordinate in both (II and (III, with overall M—O bond-length ranges of 2.694 (5–3.009 (7 (K, 2.818 (4–3.246 (4 (Rb and 2.961 (9–3.400 (10 Å (Cs. The additional three bonds in (II and (III are the result of inter-metal bridging through the water ligands. Two-dimensional coordination polymeric structures with the layers lying parallel to (100 are generated through a number of bridging bonds involving the water molecules (including hydrogen-bonding interactions, as well as through the arsanilate O atoms. These layers are linked across [100] through amine N—H...O hydrogen bonds to arsonate and water O-atom acceptors, giving overall three-dimensional network structures.

  12. [Rb(18-crown-6][Rb([2.2.2]-cryptand]Rb2Sn9·5NH3

    Stefanie Gaertner


    Full Text Available The crystal structure of the title compound, poly[[(4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosanerubidium] [[(1,4,7,10,13,16-hexaoxacyclooctadecanerubidium]di-μ-rubidium-μ-nonastannide] pentaammonia], {[Rb(C18H36N2O6][Rb3Sn9(C12H24O6C12H24O6]·5NH3}n represents the first ammoniate of a Zintl anion together with two different chelating substances, namely 18-crown-6 and [2.2.2]-cryptand. The involvement of these large molecules in the crystal structure of [Rb(18-crown-6][Rb([2.2.2]-cryptand]Rb2Sn9·5NH3 leads to the formation of a new structural motif, namely one-dimensionally extended double strands running parallel to [100] and built by Sn94− cages and Rb+ cations. The double strands are shielded by 18-crown-6 and [2.2.2]-cryptand. The cations are additionally coordinated by ammonia molecules. One of the four independent Rb+ cations is disordered over two sets of sites in a 0.74 (2:0.26 (2 ratio.

  13. Phase separation in iron chalcogenide superconductor Rb0.8+xFe1.6+ySe2 as seen by Raman light scattering and band structure calculations

    Pashkevich, Yu.; Gnezdilov, V.; Lemmens, P.; Shevtsova, T.; Gusev, A.; Lamonova, K.; Wulferding, D.; Gnatchenko, S.; Pomjakushina, E.; Conder, K.


    We report Raman light scattering in the phase separated superconducting single crystal Rb0.77Fe1.61Se2 with Tc = 32 K over a wide temperature region 3-500 K. The observed phonon lines from the majority vacancy ordered Rb2Fe4Se5 (245) antiferromagnetic phase with TN = 525 K demonstrate modest anomalies in the frequency, intensity and halfwidth at the superconductive phase transition. We identify phonon lines from the minority compressed RbδFe2Se2 (122) conductive phase. The superconducting gap with d x 2 - y 2 symmetry has been detected in our spectra. In the range 0-600 cm-1 we observe a weak but highly polarized B1g-type background which becomes well-structured upon cooling. A possible magnetic or multiorbital origin of this background is discussed. We argue that the phase separation in M0.8+xFe1.6+ySe2 is of pure magnetic origin. It occurs below the Néel temperature when the magnetic moment of iron reaches a critical value. We state that there is a spacer between the majority 245 and minority 122 phases. Using ab initio spin-polarized band structure calculations we demonstrate that the compressed vacancy ordered Rb2Fe4Se5 phase can be conductive and therefore may serve as a protective interface spacer between the purely metallic RbδFe2Se2 phase and the insulating Rb2Fe4Se5 phase providing percolative Josephson-junction like superconductivity all throughout of Rb0.8+xFe1.6+ySe2. Our lattice dynamics calculations show significant differences in the phonon spectra of the conductive and insulating Rb2Fe4Se5 phases.

  14. Structural transition induced by charge-transfer in RbMn[Fe(CN) sub 6]. Investigation by synchrotron-radiation X-ray powder analysis

    Moritomo, Y; Sakata, M; Kato, K; Kuriki, A; Tokoro, H; Ohkoshi, S I; Hashimoto, K


    Temperature dependence of atomic coordinates is determined for RbMn[Fe(CN) sub 6] by means of synchrotron-radiation (SR) X-ray powder structural analysis. We observed a structural transition from the cubic (F4-bar3m; Z=4) to the tetragonal (I4-barm2; Z=2) phase at approx. =210K in the cooling run and at approx. =300K in the warming run. In the low-temperature tetragonal phase, we found Jahn-Tellar type distortion of the MnN sub 6 octahedra and compression of the averaged Fe-C bond distance. These structural data suggest that the structural transition is triggered by the inter-metallic charge-transfer from the Mn(II) site to the Fe(III) site.

  15. Transcription of the Tumor Suppressor Genes p53 and RB in Lymphocytes from Patients with Chronic Kidney Disease: Evidence of Molecular Senescence?

    Vasileios Kordinas


    Full Text Available Patients suffering from renal failure exhibit an impaired immune system function. We wanted to investigate the transcription of the tumor suppressor genes p53 and RB to record, if these cells could be stimulated in vitro in order to divide, after the addition of antigenic and inflammatory factors. This expression was measured by real-time PCR in peripheral blood mononuclear cells (PBMCs from three different groups: ten healthy individuals, ten patients with chronic kidney disease (CKD, and ten dialysis patients with end stage renal disease (ESRD. The transcription rate of these genes was also measured after the cultivation of PBMCs under four different conditions: just with the culture medium, with lipopolysaccharide (LPS, with C-reactive protein (CRP, and with lipoxin A4 (LXA4-LPS. Our results show that in most cases after the cultivation with additives, the transcription levels were higher in dialysis patients compared to those of the other two groups. Our findings serve as indications of cellular senescence on a molecular level, while it seems that these cells are less easily stimulated in vitro in order to duplicate.

  16. Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase

    Reha-Krantz, Linda J.; Hariharan, Chithra; Subuddhi, Usharani; Xia, Shuangluo; Zhao, Chao; Beckman, Jeff; Christian, Thomas; Konigsberg, William (Yale); (Alberta)


    The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased 'breathing' at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.

  17. Proteomic analysis of pRb loss highlights a signature of decreased mitochondrial oxidative phosphorylation.

    Nicolay, Brandon N; Danielian, Paul S; Kottakis, Filippos; Lapek, John D; Sanidas, Ioannis; Miles, Wayne O; Dehnad, Mantre; Tschöp, Katrin; Gierut, Jessica J; Manning, Amity L; Morris, Robert; Haigis, Kevin; Bardeesy, Nabeel; Lees, Jacqueline A; Haas, Wilhelm; Dyson, Nicholas J


    The retinoblastoma tumor suppressor (pRb) protein associates with chromatin and regulates gene expression. Numerous studies have identified Rb-dependent RNA signatures, but the proteomic effects of Rb loss are largely unexplored. We acutely ablated Rb in adult mice and conducted a quantitative analysis of RNA and proteomic changes in the colon and lungs, where Rb(KO) was sufficient or insufficient to induce ectopic proliferation, respectively. As expected, Rb(KO) caused similar increases in classic pRb/E2F-regulated transcripts in both tissues, but, unexpectedly, their protein products increased only in the colon, consistent with its increased proliferative index. Thus, these protein changes induced by Rb loss are coupled with proliferation but uncoupled from transcription. The proteomic changes in common between Rb(KO) tissues showed a striking decrease in proteins with mitochondrial functions. Accordingly, RB1 inactivation in human cells decreased both mitochondrial mass and oxidative phosphorylation (OXPHOS) function. RB(KO) cells showed decreased mitochondrial respiratory capacity and the accumulation of hypopolarized mitochondria. Additionally, RB/Rb loss altered mitochondrial pyruvate oxidation from (13)C-glucose through the TCA cycle in mouse tissues and cultured cells. Consequently, RB(KO) cells have an enhanced sensitivity to mitochondrial stress conditions. In summary, proteomic analyses provide a new perspective on Rb/RB1 mutation, highlighting the importance of pRb for mitochondrial function and suggesting vulnerabilities for treatment.

  18. Chromatin structure regulates gene conversion.

    W Jason Cummings


    Full Text Available Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205, expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.

  19. Crystal structures and topological aspects of the high-temperature phases and decomposition products of the alkali-metal oxalates M2[C2O4] (M=K, Rb, Cs).

    Dinnebier, Robert E; Vensky, Sascha; Jansen, Martin; Hanson, Jonathan C


    The high-temperature phases of the alkali-metal oxalates M2[C2O4] (M = K, Rb, Cs), and their decomposition products M2[CO3] (M = K, Rb, Cs), were investigated by fast, angle-dispersive X-ray powder diffraction with an image-plate detector, and also by simultaneous differential thermal analysis (DTA)/thermogravimetric analysis (TGA)/mass spectrometry (MS) and differential scanning calorimetry (DSC) techniques. The following phases, in order of decreasing temperature, were observed and crystallographically characterized (an asterisk denotes a previously unknown modification): *alpha-K2[C2O4], *alpha-Rb2[C2O4], *alpha-Cs2[C2O4], alpha-K2[CO3], *alpha-Rb2[CO3], and *alpha-Cs2[CO3] in space group P6(3)/mmc; *beta-Rb2[C2O4], *beta-Cs2[C2O4], *beta-Rb2[CO3], and *beta-Cs2[CO3] in Pnma; gamma-Rb2[C2O4], gamma-Cs[C2O4], gamma-Rb2[CO3], and gamma-Cs2[CO3] in P2(1)/c; and delta-K2[C2O4] and delta-Rb2[C2O4] in Pbam. With respect to the centers of gravity of the oxalate and carbonate anions, respectively, the crystal structures of all known alkali-metal oxalates and carbonates belong to the AlB2 family, and adopt either the AlB2 or the Ni2In arrangement depending on the size of the cation and the temperature. Despite the different sizes and constitutions of the carbonate and oxalate anions, the high-temperature phases of the alkali-metal carbonates M2[CO3] (M = K, Rb, Cs), exhibit the same sequence of basic structures as the corresponding alkali-metal oxalates. The topological aspects and order-disorder phenomena at elevated temperature are discussed.

  20. RbYb(PO34

    Hui Chen


    Full Text Available Rubidium ytterbium(III tetrakis(polyphosphate, RbYb(PO34, was synthesized by solid-state reaction. It adopts structure type IV of the MRE(PO34 (M = alkali metal and RE = rare earth metal family of compounds. The structure is composed of a three-dimensional framework made up from double spiral polyphosphate chains parallel to [10-1] and irregular [YbO8] polyhedra. There are eight PO4 tetrahedra in the repeat unit of the polyphosphate chains. The Rb+ cation is located in channels extending along [100] that are delimited by the three-dimensional framework. It is surrounded by 11 O atoms, defining an irregular polyhedron.

  1. Electronic structure and optical properties of rare earth hexaborides RB{sub 6} (R = La, Ce, Pr, Nd, Sm, Eu, Gd)

    Singh, Nirpendra [Department of Physics, Indian Institute of Technology Roorkee, Roorkee-247667 (India); Saini, Sapan Mohan [Department of Physics, Indian Institute of Technology Roorkee, Roorkee-247667 (India); Nautiyal, Tashi [Department of Physics, Indian Institute of Technology Roorkee, Roorkee-247667 (India); Auluck, S [Department of Physics, Indian Institute of Technology Roorkee, Roorkee-247667 (India)


    The optical and electronic properties of the rare earth hexaborides RB{sub 6} (R = La, Ce, Pr, Nd, Sm, Eu, Gd) are studied using the full potential linearized augmented plane wave method. To account better for the on-site f-electron correlation, we adopted the Coulomb corrected local spin density approximation (LSDA+U) to the exchange correlation functional in the calculations. Our electronic structure calculation shows the overlapping of R 5d states and B 2p states at the X symmetry point. The magnetic moment of the ferromagnetic rare earth hexaborides increases with increasing 4f occupation. The calculated reflectivity and optical conductivity spectra are in agreement with the experimental data, although the structures in the calculated optical spectra are sharper.

  2. Structure and magnetism in hexagonal tungsten bronze metal oxides AM1/3W8/3O9 (A-K, Rb, Cs; M-Cr, Fe)

    Ivanov, S. A.; Sahu, J. R.; Voronkova, V. I.; Mathieu, R.; Nordblad, P.


    The structure and magnetic properties of hexagonal tungsten bronzes AM1/3W8/3O9 (A-K+, Rb+, Cs+; M- Cr3+, Fe3+) have been investigated. Pure ceramic samples were synthesized by solid-state reaction. The samples have been studied by X-ray powder diffraction in combination with magnetic measurements. The compounds crystallize in hexagonal space group P63/mcm. The substitution of magnetic ions into the WO6 octahedra yields dilute antiferromagnetic Cr3+-O2--Cr3+ (or Fe3+-O2--Fe3+) superexchange interaction causing the appearance of short-range magnetic order at low temperatures. The antiferromagnetic character of the interaction is supported by negative values of the derived Curie-Weiss temperatures, θCW. The magnitude of θCW is found to decrease with increasing ionic radius of the A cation.

  3. Giant magnetoresistance of novel ferromagnets AMg4Mn6O15 (A=K, Rb, and Cs) with highly symmetric structure

    Tanaka, Yudai; Sato, Hirohiko


    A novel family of cubic manganese oxides, AMg4Mn6O15 (A=K, Rb, and Cs), were discovered. In this type of structure, the MnO6 octahedra share edges, constructing a highly symmetric framework where Mn atoms form a three-dimensional network of truncated octahedra. The crystallographic site of Mn is unique and the average oxidation state of Mn is 3.5, indicating a mixed-valence electronic state where Mn3+ and Mn4+ sites are completely indistinguishable. These compounds become ferromagnetic with fully polarized magnetic moments of Mn ions. The ferromagnetic transition temperature TC is 170 K, that is considerably high for manganese oxides. The electric resistivity of KMg4Mn6O15 is about 105 Ωcm at 300 K and exhibits a non-metallic temperature dependence. It reveals a large negative magnetoresistance; about 40% of the resistivity is suppressed by 5 T of magnetic field at TC.

  4. MADS-box gene evolution - structure and transcription patterns

    Johansen, Bo; Pedersen, Louise Buchholt; Skipper, Martin;


    Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs......Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs...

  5. Instability of a quasi-magnetic structure in a layer compound, Cs{sub 0.5}Rb{sub 0.5}VF{sub 4}

    Hidaka, M.; Yoshimura, M. [Department of Physics, Faculty of Sciences, Kyushu University, Fukuoka 812-8581 (Japan); Akiyama, H. [Department of Physics, Faculty of Education, Miyazaki University, Miyazaki 889-21 (Japan); Watanabe, S.; Yoshizawa, H. [Neutron scattering Laboratory, ISSP, University of Tokyo, Tokai, Ibaraki 319-1106 (Japan); Wanklyn, B.M. [Claredon Laboratory, Oxford University, Oxford OX1 3PU (United Kingdom)


    Magnetic properties of Cs{sub 0.5}Rb{sub 0.5}VF{sub 4} are studied by neutron diffraction. The layer compound shows an antiferromagnetic phase transition at about 34 K (T{sub N}). Its normal antiferromagnetic unit cell is 2a{sub p} x 2b{sub p} x 2c{sub p}, where a{sub p} x a{sub p} x c{sub p} is an ideal unit cell of TlAlF{sub 4}-type. It is found that a quasi-antiferromagnetic phase having a unit cell of 2a{sub p} x 2a{sub p} x c{sub p} is easily induced under a suitable applied field after doing a field cooling of 3 T from 50 K to 2.5 K. The quasi-magnetic structure shows a relaxation dependent on the field strength and the temperature. In the relaxation process, it is found that there is a coexistence of the normal and quasi-antiferromagnetic phases and that the two magnetic phases show a good compensation for a population ratio between two phases made in a used crystal. A metastable magnetic phase transition between the normal and quasi-magnetic phases occurs at about 13 K (T{sub M}). It is also found that only the quasi-magnetic phase shows a critical behavior in the vicinity of the antiferromagnetic phase transition (T{sub N}). It is interpreted that the residual normal antiferromagnetic phases below T{sub M} are made by local structural modulations, which mainly result from an inhomogeneous substitution of Cs with Rb ions in the crystal. (orig.)

  6. One-pot occurrence of two polymorphs of Rb2Sc[Si4O10]F and their structural, spectroscopic and computational characterization

    Kahlenberg, Volker; Manninger, Tanja; Perfler, Lukas; Többens, Daniel M.


    Single-crystal growth experiments in the system RbF-Sc2O3-SiO2 resulted in the crystallization of two forms of Rb2Sc[Si4O10]F within the same run. Basic crystallographic data of the two concomitant polymorphs at ambient conditions are as follows: phase I: space group I4/m, a=11.2619(3) Å, c=8.3053(4) Å, V=1053.36(6) Å3, Z=4; phase II: space group P21/m, a=11.5085(6) Å, b=8.3805(3) Å, c=11.6750(6) Å, β=111.147(6)°, V=1050.19(9) Å3, Z=4. The structures were determined by direct methods and refined to residuals of R(|F|)=0.0231 (phase I) for 516 and 0.0249 (phase II) for 2050 independent observed reflections with I>2σ(I). Phase I showed twinning by merohedry which was accounted for during the refinement process. Both compounds are based on multiple chains of [SiO4]-tetrahedra forming closed columns or tubes. The multiplicity of the unbranched fundamental chains is two (for phase I) and four (for phase II), respectively. The periodicity of the multiple chains has a value of four in both modifications which is also reflected in similar translation periods along the chain directions (phase I: t[001]=8.31 Å; phase II: t[010]=8.38 Å). Alternatively, both polymorphs can be described as mixed octahedral-tetrahedral frameworks, which can be classified according to their polyhedral microensembles. A topological analysis of both networks is presented. Structural investigations have been supplemented by micro-Raman spectroscopy. The interpretation of the spectroscopic data including the allocation of the bands to certain vibrational species has been aided by DFT-calculations.

  7. Overlapping and distinct pRb pathways in the mammalian auditory and vestibular organs.

    Huang, Mingqian; Sage, Cyrille; Tang, Yong; Lee, Sang Goo; Petrillo, Marco; Hinds, Philip W; Chen, Zheng-Yi


    Retinoblastoma gene (Rb1) is required for proper cell cycle exit in the developing mouse inner ear and its deletion in the embryo leads to proliferation of sensory progenitor cells that differentiate into hair cells and supporting cells. In a conditional hair cell Rb1 knockout mouse, Pou4f3-Cre-pRb(-/-), pRb(-/-) utricular hair cells differentiate and survive into adulthood whereas differentiation and survival of pRb(-/-) cochlear hair cells are impaired. To comprehensively survey the pRb pathway in the mammalian inner ear, we performed microarray analysis of (pRb(-/-) cochlea and utricle. The comparative analysis shows that the core pathway shared between pRb(-/-) cochlea and utricle is centered on E2F, the key pathway that mediates pRb function. A majority of differentially expressed genes and enriched pathways are not shared but uniquely associated with pRb(-/-) cochlea or utricle. In pRb(-/-) cochlea, pathways involved in early inner ear development such as Wnt/β-catenin and Notch were enriched, whereas pathways involving in proliferation and survival are enriched in pRb(-/-) utricle. Clustering analysis showed that the pRb(-/-) inner ear has characteristics of a younger control inner ear, an indication of delayed differentiation. We created a transgenic mouse model (ER-Cre-pRb(flox/flox)) in which Rb1 can be acutely deleted postnatally. Acute Rb1 deletion in the adult mouse fails to induce proliferation or cell death in inner ear, strongly indicating that Rb1 loss in these postmitotic tissues can be effectively compensated for, or that pRb-mediated changes in the postmitotic compartment result in events that are functionally irreversible once enacted. This study thus supports the concept that pRb-regulated pathways relevant to hair cell development, encompassing proliferation, differentiation and survival, act predominantly during early development.

  8. Vibrio cholerae VttRA and VttRB Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island

    Chaand, Mudit; Dziejman, Michelle


    A subset of non-O1/non-O139 serogroup strains of Vibrio cholerae cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ∼50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttRA and VttRB, which are ToxR homologues. Previous experiments demonstrated that VttRA and VttRB are necessary for colonization in vivo and promote bile-dependent T3SS gene expression in vitro. To better unders...

  9. Vibrio cholerae VttRA and VttRB Regulatory Influences Extend beyond the Type 3 Secretion System Genomic Island

    Chaand, Mudit; Dziejman, Michelle


    A subset of non-O1/non-O139 serogroup strains of Vibrio cholerae cause disease using type 3 secretion system (T3SS)-mediated mechanisms. An ∼50-kb genomic island carries genes encoding the T3SS structural apparatus, effector proteins, and two transmembrane transcriptional regulators, VttRA and VttRB, which are ToxR homologues. Previous experiments demonstrated that VttRA and VttRB are necessary for colonization in vivo and promote bile-dependent T3SS gene expression in vitro. To better unders...

  10. RB, the conductor that orchestrates life, death and differentiation.

    Khidr, L; Chen, P-L


    The retinoblastoma susceptibility gene was the first tumor suppressor gene identified in humans and the first tumor suppressor gene knocked out by targeted deletion in mice. RB serves as a transducer between the cell cycle machinery and promoter-specific transcription factors, its most documented activity being the repression of the E2F family of transcription factors, which regulate the expression of genes involved in cell proliferation and survival. Recent investigations of RB function suggest that it works as a fundamental regulator to coordinate pathways of cellular growth and differentiation. In this review, we unravel the novel role of an equally important aspect of RB in downregulating the differentiation inhibitor EID-1 during cellular differentiation by teasing apart the signal, which elicit differentiation and limit cell cycle progression, since the molecular mechanisms relating to RB activation of differentiation is much less understood. We review the various roles for RB in differentiation of neurons, muscle, adipose tissue, and the retina. In addition, we provide an update for the current models of the role of RB in cell cycle to entry and exit, extending the view toward chromatin remodeling and expose the dichotomies in the regulation of RB family members. We conclude with a discussion of a novel RB regulatory network, incorporating the dynamic contribution of EID family proteins.


    苏长青; 叶玉坤; 汪栋; 曹祥荣; 单祥年


    The authors used immunohistochemistry and in situ hybridization to observe the expression of the p16 and Rb mRNA and protein levels in 89 cases of lung cancer. The results showed that the loss of p16 gene expression took place mainly in non-small cell lung cancer, and loss of Rb gene expression mainly in small cell lung cancer. The expression of these genes on protein level fundamentally corresponded with mRNA level. It is suggested that the expression of these two genes are related to the histological type of lung cancer, and the p16 and Rb genes can be considered as one of molecular biological targets for gene classification diagnosis. There may exist a mechanism at gene translation level which leads to the inactivation of the p16 and Rb genes.%为研究p16和Rb基因在蛋白水平和mRNA水平的表达及其与肺癌发生发展的关系,采用免疫组化和原位杂交的方法,对89例肺癌手术标本进行了p16和Rb基因表达的定位观察。发现p16基因蛋白的丢失主要发生于非小细胞肺癌,Rb基因蛋白的丢失主要发生于小细胞肺癌。两种基因各自在蛋白水平和mRNA水平的表达基本相符。提示p16和Rb基因的表达与肺癌的组织学类型密切相关,有可能作为非小细胞肺癌与小细胞肺癌基因分型诊断的分子生物学指标之一;在翻译水平上也存在着引起基因失活的可能机制。

  12. Crystal structures of MBi{sub 2}Br{sub 7} (M = Rb, Cs) - filled variants of AX{sub 7} sphere packing

    Chang, Jen-Hui; Wolff, Alexander [Fachrichtung Chemie und Lebensmittelchemie, Technische Universitaet Dresden, 01062 Dresden (Germany); Ruck, Michael [Fachrichtung Chemie und Lebensmittelchemie, Technische Universitaet Dresden, 01062 Dresden (Germany); Max-Planck-Institut fuer Chemische Physik fester Stoffe, Noethnitzer Str. 40, 01187 Dresden (Germany)


    The reinvestigation of the pseudo-binary systems MBr-BiBr{sub 3} (M = Rb, Cs) revealed two new phases with composition MBi{sub 2}Br{sub 7}. Both compounds are hygroscopic and show brilliant yellow color. The crystal structures were solved from X-ray single crystal diffraction data. The isostructural compounds adopt a new structure type in the triclinic space group P anti 1. The lattice parameters are a = 755.68(3) pm, b = 952.56(3) pm, c = 1044.00(4) pm, α = 76.400(2) , β = 84.590(2) , γ = 76.652(2) for RbBi{sub 2}Br{sub 7} and a = 758.71(5) pm, b = 958.23(7) pm, c = 1060.24(7) pm, α = 76.194(3) , β = 83.844(4) , γ = 76.338(3) for CsBi{sub 2}Br{sub 7}. The crystal structures consist of M{sup +} cations in anticuboctahedral coordination by bromide ions and bromidobismuthate(III) layers {sup 2}{sub ∞}[Bi{sub 2}Br{sub 7}]{sup -}. The 2D layers comprise pairs of BiBr{sub 6} octahedra sharing a common edge. The Bi{sub 2}Br{sub 10} double octahedra are further connected by common vertices. The bismuth(III) atoms increase their mutual distance in the double octahedra by off-centering so that the BiBr{sub 6} octahedra are distorted. The CsBi{sub 2}Br{sub 7} type can be interpreted as a common hexagonal close sphere packing of M and Br atoms, in which 1/4 of the octahedral voids are filled by Bi atoms. The structure type was systematically analyzed and compared with alternative types of common packings. The existence of a compound with the suggested composition CsBiBr{sub 4} could not be verified experimentally. (Copyright copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor.

    Carr, Simon M; Munro, Shonagh; Zalmas, Lykourgos-Panagiotis; Fedorov, Oleg; Johansson, Catrine; Krojer, Tobias; Sagum, Cari A; Bedford, Mark T; Oppermann, Udo; La Thangue, Nicholas B


    The retinoblastoma tumor suppressor protein pRb is a key regulator of cell cycle progression and mediator of the DNA damage response. Lysine methylation at K810, which occurs within a critical Cdk phosphorylation motif, holds pRb in the hypophosphorylated growth-suppressing state. We show here that methyl K810 is read by the tandem tudor domain containing tumor protein p53 binding protein 1 (53BP1). Structural elucidation of 53BP1 in complex with a methylated K810 pRb peptide emphasized the role of the 53BP1 tandem tudor domain in recognition of the methylated lysine and surrounding residues. Significantly, binding of 53BP1 to methyl K810 occurs on E2 promoter binding factor target genes and allows pRb activity to be effectively integrated with the DNA damage response. Our results widen the repertoire of cellular targets for 53BP1 and suggest a previously unidentified role for 53BP1 in regulating pRb tumor suppressor activity.

  14. 鸡视网膜母细胞瘤基因1(RB1)多态性与体重性状的相关性%Association of single nucleotide polymorphism of RB1 gene with body weight traits in chicken

    陈曦; 张慧; 王宇祥; 王守志; 程博涵; 李辉


    为探讨鸡视网膜母细胞瘤基因1(Retinoblastoma1,RB1)多态性对体重性状的影响,文章以东北农业大学高、低脂双向选择品系肉鸡为实验材料,采用MALDI-TOF-MS 、PCR-RFLP 方法进行基因多态性检测和个体基因型分析,共获得27 个SNP 位点的基因型数据.采用滑动窗口法构建单倍型,进而利用单位点和单倍型分别与鸡体重性状进行关联分析.结合单位点和单倍型分析结果,确定了RB1 基因上4 个显著影响1 周龄体重的SNP 位点,2 个显著影响1、3 周龄体重的SNP 位点.研究结果表明RB1 基因是影响鸡早期体重性状的重要候选基因.%The Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used in the current study to investigate the effects of Retinoblastomal (RBI) gene on chicken body weight (BW). The single nucleotide polymorphisms (SNPs) of the individuals were detected by MALDI-TOF-MS and PCR-RFLP methods and the genotypes of 27 SNPs were obtained. Haplotypes were constructed by liding window approach. Association analysis between single SNPs and haplotypes and body weight were conducted, respectively. Based on the results of single SNPs and haplotype association analyses. Four SNPs with significant effects on body weight at 1 week of age (BW1) and 2 SNPs with significant effects on BW1 and BW3 were determined. These results suggested that RB1 is an important candidate gene that affects chicken early growth and development.

  15. Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells.

    Váraljai, Renáta; Islam, Abul B M M K; Beshiri, Michael L; Rehman, Jalees; Lopez-Bigas, Nuria; Benevolenskaya, Elizaveta V


    The retinoblastoma tumor suppressor protein pRb restricts cell growth through inhibition of cell cycle progression. Increasing evidence suggests that pRb also promotes differentiation, but the mechanisms are poorly understood, and the key question remains as to how differentiation in tumor cells can be enhanced in order to diminish their aggressive potential. Previously, we identified the histone demethylase KDM5A (lysine [K]-specific demethylase 5A), which demethylates histone H3 on Lys4 (H3K4), as a pRB-interacting protein counteracting pRB's role in promoting differentiation. Here we show that loss of Kdm5a restores differentiation through increasing mitochondrial respiration. This metabolic effect is both necessary and sufficient to induce the expression of a network of cell type-specific signaling and structural genes. Importantly, the regulatory functions of pRB in the cell cycle and differentiation are distinct because although restoring differentiation requires intact mitochondrial function, it does not necessitate cell cycle exit. Cells lacking Rb1 exhibit defective mitochondria and decreased oxygen consumption. Kdm5a is a direct repressor of metabolic regulatory genes, thus explaining the compensatory role of Kdm5a deletion in restoring mitochondrial function and differentiation. Significantly, activation of mitochondrial function by the mitochondrial biogenesis regulator Pgc-1α (peroxisome proliferator-activated receptor γ-coactivator 1α; also called PPARGC1A) a coactivator of the Kdm5a target genes, is sufficient to override the differentiation block. Overexpression of Pgc-1α, like KDM5A deletion, inhibits cell growth in RB-negative human cancer cell lines. The rescue of differentiation by loss of KDM5A or by activation of mitochondrial biogenesis reveals the switch to oxidative phosphorylation as an essential step in restoring differentiation and a less aggressive cancer phenotype.

  16. Structural, electronic and thermodynamic properties of R{sub 3}ZnH{sub 5} (R=K, Rb, Cs): A first-principle calculation

    Li, Jia; Zhang, Shengli [Division of Molecule and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Huang, Shiping, E-mail: [Division of Molecule and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Wang, Peng; Tian, Huiping [Research Institute of Petroleum Processing, SINOPEC , Beijing 100083 (China)


    R{sub 3}ZnH{sub 5} (R=K, Rb, Cs) series have been investigated with respect to the crystal structure, electronic and thermodynamic properties using first-principle methods based on density functional theory with generalized gradient approximation. The optimized structures and atomic coordinates are in good agreement with the experimental data. The strong covalent interactions are obtained between Zn and H atoms in the 18-electron [ZnH{sub 4}]{sup 2-} complex, while an ionic interaction is found between [ZnH{sub 4}]{sup 2-} and R atom. The formation enthalpies show that the formations of R{sub 3}ZnH{sub 5} hydrides are all exothermic at 298 K. The vibration free energies of R{sub 3}ZnH{sub 5} show that the thermodynamic stabilities of R{sub 3}ZnH{sub 5} hydrides decrease with the increasing diameter of R atom. Two possible decomposition reactions of R{sub 3}ZnH{sub 5} series have been suggested in our work. One (reaction one) is that R{sub 3}ZnH{sub 5} hydrides decomposes to elements directly, and the other (reaction two) is that R{sub 3}ZnH{sub 5} hydrides decomposes to RH hydride. The results show that the first decomposition reaction is more favorable one. The spontaneous decomposition reaction of K{sub 3}ZnH{sub 5} hydrides occur upon 465 K via reaction one, and 564 K via reaction two, respectively. - Graphical abstract: Total charge density of K{sub 3}ZnH{sub 5}. Highlights: Black-Right-Pointing-Pointer Electronic and thermodynamic properties of R{sub 3}ZnH{sub 5} (R=K, Rb, Cs) were calculated. Black-Right-Pointing-Pointer The formations of R{sub 3}ZnH{sub 5} hydrides are all exothermic at 298 K. Black-Right-Pointing-Pointer The thermodynamic stabilities decrease with the increasing diameter of R atom. Black-Right-Pointing-Pointer Two possible decomposition pathways of R{sub 3}ZnH{sub 5} were investigated.

  17. Dual Loss of Rb1 and Trp53 in the Adrenal Medulla Leads to Spontaneous Pheochromocytoma

    Ian D. Tonks


    Full Text Available Using a Cre/loxP system, we have determined the phenotypic consequences attributable to in vivo deletion of both Rb1 and Trp53 in the mouse adrenal medulla. The coablation of these two tumor suppressor genes during embryogenesis did not disrupt adrenal gland development but resulted in the neoplastic transformation of the neural crest-derived adrenal medulla, yielding pheochromocytomas (PCCs that developed with complete penetrance and were inevitably bilateral. Despite their typically benign status, these PCCs had profound ramifications on mouse vitality, with effected mice having a median survival of only 121 days. Evaluation of these PCCs by both immunohistochemistry and electron microscopy revealed that most Rb1-/-:Trp53-/- chromaffin cells possessed atypical chromagenic vesicles that did not seem capable of appropriately storing synthesized catecholamines. The structural remodeling of the heart in mice harboring Rb1-/-:Trp53-/- PCCs suggests that the mortality of these mice may be attributable to the inappropriate release of catecholamines from the mutated adrenal chromaffin cells. On the basis of the collective data from Rb1 and Trp53 knockout mouse models, it seems that the conversion of Rb1 loss-driven adrenal medulla hyperplasia to PCC can be greatly enhanced by the compound loss of Trp53, whereas the loss of Trp53 alone is generally ineffectual on adrenal chromaffin cell homeostasis. Consequently, the Trp53 tumor suppressor gene is an efficient genetic modifier of Rb1 loss in the development of PCC, and their compound loss in the adrenal medulla has a profound impact on both cellular homeostasis and animal vitality.

  18. Structure of the murine Thy-1 gene

    V. Giguere; K-I. Isobe; F.G. Grosveld (Frank)


    textabstractWe have cloned the murine Thy-1.1 (AKR) and Thy-1.2 (Balb/c) genes. The complete exon/intron structure and the nucleotide sequence of the Thy-1.2 gene was determined. The gene contains four exons and three intervening sequences. The complete transcriptional unit gives rise to a tissue an

  19. Structures and Conductivities of the Quaternary A/Bi/Cu/S Phases KBi 2CuS 4 and A3Bi 5Cu 2S 10 ( A=Rb, Cs)

    Yang, Yuting; Brazis, Paul; Kannewurf, Carl R.; Ibers, James A.


    The compounds KBi2CuS4, Cs3Bi5Cu2S10, and Rb3Bi5Cu2S10 were prepared by stoichiometric reactions of the corresponding alkali-metal sulfides with Bi, Cu, and S at 1123 K. KBi2CuS4 crystallizes as a racemic twin in space group Cmc21 of the orthorhombic system with four formula units in a cell of dimensions a=4.0273(8), b=13.770(3), c=14.259(3) Å at 153 K; A3Bi5Cu2S10 (A=Cs or Rb) are isostructural and crystallize in a new structure type in space group Pnnm with two formula units in cells of dimensions a=14.571(3), b=17.819(4), c=4.0686(8) Å for Rb3Bi5Cu2S10 and a=15.041(3), b=17.994(3), c=4.0973(8) Å for Cs3Bi5Cu2S10 at 153 K. These are channel structures with the alkali-metal cations located in channels formed by edge sharing of distorted Bi octahedra and distorted Cu tetrahedra. Electrical conductivity measurements on KBi2CuS4 and Rb3Bi5Cu2S10 indicate that both materials are semiconducting. The conductivity of KBi2CuS4 is two orders of magnitude higher than that of Rb3Bi5Cu2S10 at room temperature. KBi2CuS4 undergoes a transition from an n- to a p-type semiconductor at 210 K as determined by thermopower measurements.

  20. More epigenetic hits than meets the eye: microRNAs and genes associated with the tumorigenesis of retinoblastoma

    Adriana H.O. Reis


    Full Text Available Retinoblastoma (RB, a childhood neoplasia of the retinoblasts, can occur unilaterally or bilaterally, with one or multiple foci per eye. RB is associated with somatic loss-of-function of both alleles of the tumor suppressor gene RB1. Hereditary forms emerge due to germline loss-of-function mutations in RB1 alleles. RB has long been the prototypic ‘‘model’’ cancer ever since Knudson’s ‘‘two-hit’’ hypothesis. However, a simple two-hit model for RB is challenged by an increasing number of studies documenting additional hits that contribute to RB development. Here we review the genetics and epigenetics of RB with a focus on the role of small noncoding RNAs (microRNAs and on novel findings indicating the relevance of DNA methylation in the development and prognosis of this neoplasia. Studies point to an elaborated landscape of genetic and epigenetic complexity, in which a number of events and pahtways play crucial roles in the origin and prognosis of RB. These include roles for microRNAs, inprinted loci, and parent-of-origin contributions to RB1 regulation and RB progression. This complexity is also manifested in the structure of the RB1 locus itself: it includes numerous repetitive DNA segments and retrotransposon insertion elements, some of which are actively transcribed from the RB1 locus. Altogether, we conclude that RB1 loss of function represents the tip of an iceberg of events that determine RB development, progression, severity, and disease risk. Comprehensive assessment of personalized RB risk will require genetic and epigenetic evaluations beyond RB1 protein coding sequences.

  1. Synthesis and structure of (Rb{sub 0.50}Ba{sub 0.25})[UO{sub 2}(CH{sub 3}COO){sub 3}

    Serezhkina, L. B., E-mail: [Samara State University (Russian Federation); Peresypkina, E. V.; Virovets, A. V. [Russian Academy of Sciences, Institute of Inorganic Chemistry, Siberian Branch (Russian Federation); Klepov, V. V. [Samara State University (Russian Federation)


    A new compound (Rb{sub 0.50}Ba{sub 0.25})[UO{sub 2}(CH{sub 3}COO){sub 3}] is synthesized and its crystal structure is studied by X-ray diffraction. The compound crystallizes in the form of yellow plates belonging to the cubic crystal system. The unit cell parameter a = 17.0367(1) A, V = 4944.89(5) A{sup 3}, space group I 4 bar 3d, Z = 16, and R = 0.0182. The coordination polyhedron of the uranium atom is a hexagonal bipyramid with oxygen atoms of three acetate groups and the uranyl group in the vertices. The crystal chemical formula of the uranium-containing group is AB{sub 3}{sup 01}(A = UO{sub 2}{sup 2+}, B{sup 01} = CH{sub 3}COO{sup -}). The oxygen atoms of the acetate groups that enter the coordination polyhedron of uranium are bound to barium and rubidium atoms.

  2. Gene function prediction based on the Gene Ontology hierarchical structure.

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao


    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  3. Synthesis, characterization and crystal structure of a novel Strandberg-type polyoxoselenomolybdate Rb{sub 4}[Se{sub 2}Mo{sub 5}O{sub 21}]{center_dot}2H{sub 2}O

    Nagazi, Ichraf, E-mail: [Departement de Chimie, Institut Superieur des Mathematiques Appliquees et d' Informatique, Avenue Assad Iben Fourat, 3100 Kairouan (Tunisia); Haddad, Amor [Laboratoire des Materiaux et Cristallochimie (LMC), Institut Superieur des Sciences Appliquees et Technologie, Avenue El Mourouj, 5111 Mahdia (Tunisia)


    Graphical abstract: Crystal structure of Rb{sub 4}[Se{sub 2}Mo{sub 5}O{sub 21}]{center_dot}2H2O. Highlights: Black-Right-Pointing-Pointer Synthesis of the first Strandberg-type polyoxoselenomolybdate Rb{sub 4}[Se{sub 2}Mo{sub 5}O{sub 21}]{center_dot}2H{sub 2}O. Black-Right-Pointing-Pointer Characterization of the novel compound. Black-Right-Pointing-Pointer Chirality of the space group C2 of compound implies that it is expected to have nonlinear optical (NLO) properties -- Abstract: An inorganic compound formulated as Rb{sub 4}[Se{sub 2}Mo{sub 5}O{sub 21}]{center_dot}2H{sub 2}O (1) has been isolated by conventional solution method and structurally characterized by single-crystal X-ray diffraction methods, scanning electron microscopy (SEM), powder XRD, IR, UV-vis spectra, and cyclic voltammetry measurements. This compound crystallizes in the monoclinic system, space group C2 with unit a = 19.701 (3) Angstrom-Sign , b = 10.296 (2) Angstrom-Sign , c = 12.134 (4) Angstrom-Sign , {beta} = 106.96 (2) Degree-Sign and Z = 4. The crystal structure of (1) is built up from a Strandberg clusters connected through hydrogen-bonding interactions into a three-dimensional supramolecular network.

  4. Preparation and structural properties of nonlinear optical borates K{sub 2(1-x)}Rb{sub 2x}Al{sub 2}B{sub 2}O{sub 7}, 0 < x < 0.75

    Atuchin, V.V., E-mail: [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Bazarov, B.G. [Laboratory of Oxide Systems, Baikal Institute of Nature Management, SB RAS, Ulan-Ude 47, 670047 (Russian Federation); Gavrilova, T.A. [Laboratory of Nanodiagnostics and Nanolithography, Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090 (Russian Federation); Grossman, V.G. [Laboratory of Oxide Systems, Baikal Institute of Nature Management, SB RAS, Ulan-Ude 47, 670047 (Russian Federation); Molokeev, M.S. [Laboratory of Crystal Physics, Institute of Physics, SB RAS, Krasnoyarsk 660036 (Russian Federation); Bazarova, Zh.G. [Laboratory of Oxide Systems, Baikal Institute of Nature Management, SB RAS, Ulan-Ude 47, 670047 (Russian Federation)


    Highlights: Black-Right-Pointing-Pointer Solid solutions K{sub 2(1-x)}Rb{sub 2x}Al{sub 2}B{sub 2}O{sub 7} are synthesized over wide composition range up to x {approx} 0.83. Black-Right-Pointing-Pointer Crystal structure of K{sub 2(1-x)}Rb{sub 2x}Al{sub 2}B{sub 2}O{sub 7} solutions is determined in space group P321. Black-Right-Pointing-Pointer Second harmonic generation is observed in KRbAl{sub 2}B{sub 2}O{sub 7}. Black-Right-Pointing-Pointer Drastic variation of cell parameters is found over KABO-type crystal family. - Abstract: The structures of K{sub 2(1-x)}Rb{sub 2x}Al{sub 2}B{sub 2}O{sub 7}, x = 0.25, 0.5, 0.75, have been determined in space group P321 through Rietveld analysis of X-ray powder diffraction data. The solubility limit in K{sub 2(1-x)}Rb{sub 2x}Al{sub 2}B{sub 2}O{sub 7} crystals has been estimated as x {approx} 0.83-0.9. Nonlinear optical properties of KRbAl{sub 2}B{sub 2}O{sub 7} have been verified by powder Kurtz-Perry method. Mechanisms of structural parameter variation in K{sub 2}Al{sub 2}B{sub 2}O{sub 7} crystal family have been discussed.

  5. Polymer-like structures of LiSCN, NaSCN, KSCN, RbSCN, and CsSCN complexes with an armed monoaza-15-crown-5 ether bearing a 3',5'-difluoro-4'-hydroxybenzyl group.

    Habata, Yoichi; Okazaki, Chizuko; Ogura, Kinuko; Akabori, Sadatoshi; Zhang, Xian X; Bradshaw, Jerald S


    Structures of LiSCN, NaSCN, KSCN, RbSCN, and CsSCN complexes with 3',5'-difluoro-4'-hydroxybenzyl-armed monoaza-15-crown-5 ether (5) were investigated. The Li+ and Na+ complexes are (1:1)n polymer-like complexes bridged by hydrogen bonding. On the other hand, the K+, Rb+, and Cs+ complexes are polymer-like complexes bridged by the fluorine atoms of the side arms. The titration calorimetry and 19F NMR titration experiments suggest that one or both fluorine atoms along with the oxygen atom of the phenolic OH group coordinate to the alkali metal ions incorporated in the crown part of a second armed ligand to give polymer-like complexes in solution. The FAB-MS data indicated that larger alkali metal ions form more stable polymer-like complexes.

  6. Overexpression of Brucella putative glycosyltransferase WbkA in B. abortus RB51 leads to production of exopolysaccharide

    Neha eDabral


    Full Text Available Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an IS711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s containing mannose, galactose, N-acetylglucosamine and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice.

  7. Overexpression of Brucella putative glycosyltransferase WbkA in B. abortus RB51 leads to production of exopolysaccharide.

    Dabral, Neha; Jain-Gupta, Neeta; Seleem, Mohamed N; Sriranganathan, Nammalwar; Vemulapalli, Ramesh


    Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an IS711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine, and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice.

  8. Prediction of the equilibrium structures and photomagnetic properties of the Prussian blue analogue RbMn[Fe(CN)(6)] by density functional theory

    Luzon, Javier; Castro, Miguel; Vertelman, Esther J.M.; Gengler, Régis Y.N.; van Koningsbruggen, Petra J.; Molodtsova, Olga; Knupfer, Martin; Rudolf, Petra; Loosdrecht, Paul H.M. van; Broer, Ria


    A periodic density functional theory method using the B3LYP hybrid exchange-correlation potential is applied to the Prussian blue analogue RbMn[Fe(CN)(6)] to evaluate the suitability of the method for studying, and predicting, the photomagnetic behavior of Prussian blue analogues and related materia

  9. RB: Programmer Specification of Redundancy

    Smith, Jonathan M.; Gerald Q. Maguire Jr.


    RB is a programming language for specifying redundancy in various dimensions. Avizienis's notation T I HIS, for Time I Hardware I Software, describes the different types of redundancy possible in a computation: repetition (nT I HIS), redundant hardware (T I nH I S), and program (software) (T I H InS). These can each be controlled by the programmer with RB. RB derives its name from its use of the recovery block notion to specify fault-tolerant segments of software. RB also supplies the program...

  10. Deletion of autophagy inducer RB1CC1 results in degeneration of the retinal pigment epithelium.

    Yao, Jingyu; Jia, Lin; Khan, Naheed; Lin, Chengmao; Mitter, Sayak K; Boulton, Michael E; Dunaief, Joshua L; Klionsky, Daniel J; Guan, Jun-Lin; Thompson, Debra A; Zacks, David N


    Autophagy regulates cellular homeostasis and response to environmental stress. Within the retinal pigment epithelium (RPE) of the eye, the level of autophagy can change with both age and disease. The purpose of this study is to determine the relationship between reduced autophagy and age-related degeneration of the RPE. The gene encoding RB1CC1/FIP200 (RB1-inducible coiled-coil 1), a protein essential for induction of autophagy, was selectively knocked out in the RPE by crossing Best1-Cre mice with mice in which the Rb1cc1 gene was flanked with Lox-P sites (Rb1cc1(flox/flox)). Ex vivo and in vivo analyses, including western blot, immunohistochemistry, transmission electron microscopy, fundus photography, optical coherence tomography, fluorescein angiography, and electroretinography were performed to assess the structure and function of the retina as a function of age. Deletion of Rb1cc1 resulted in multiple autophagy defects within the RPE including decreased conversion of LC3-I to LC3-II, accumulation of autophagy-targeted precursors, and increased numbers of mitochondria. Age-dependent degeneration of the RPE occurred, with formation of atrophic patches, subretinal migration of activated microglial cells, subRPE deposition of inflammatory and oxidatively damaged proteins, subretinal drusenoid deposits, and occasional foci of choroidal neovascularization. There was secondary loss of photoreceptors overlying the degenerated RPE and reduction in the electroretinogram. These observations are consistent with a critical role of autophagy in the maintenance of normal homeostasis in the aging RPE, and indicate that disruption of autophagy leads to retinal phenotypes associated with age-related degeneration.

  11. A comprehensive modular map of molecular interactions in RB/E2F pathway.

    Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Radvanyi, François; Barillot, Emmanuel


    We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large-scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

  12. Carbonate hydrates of the heavy alkali metals: preparation and structure of Rb{sub 2}CO{sub 3} . 1.5 H{sub 2}O und Cs{sub 2}CO{sub 3} . 3 H{sub 2}O; Carbonat-Hydrate der schweren Alkalimetalle: Darstellung und Struktur von Rb{sub 2}CO{sub 3} . 1,5 H{sub 2}O und Cs{sub 2}CO{sub 3} . 3 H{sub 2}O

    Cirpus, V.; Wittrock, J.; Adam, A. [Koeln Univ. (Germany). Inst. fuer Anorganische Chemie


    Rb{sub 2}CO{sub 3} . 1.5 H{sub 2}O and Cs{sub 2}CO{sub 3} . 3 H{sub 2}O were prepared from aqueous solution and by means of the reaction of dialkylcarbonates with RbOH and CsOH resp. in hydrous alcoholes. Based on four-circle diffractometer data, the crystal structures were determined (Rb{sub 2}CO{sub 3} . 1.5 H{sub 2}O: C2/c (no. 15), Z = 8, a = 1237.7(2) pm, b = 1385.94(7) pm, c = 747.7(4) pm, {beta} = 120.133(8) , V{sub EZ} = 1109.3(6) . 10{sup 6} pm{sup 3}; Cs{sub 2}CO{sub 3} . 3 H{sub 2}O: P2/c (no. 13), Z = 2, a = 654.5(2) pm, b = 679.06(6) pm, c = 886.4(2) pm, {beta} = 90.708(14) , V{sub EZ} = 393.9(2) . 10{sup 6} pm{sup 3}). Rb{sub 2}CO{sub 3} . 1.5 H{sub 2}O is isostructural with K{sub 2}CO{sub 3} . 1.5 H{sub 2}O. In case of Cs{sub 2}CO{sub 3} . 3 H{sub 2}O no comparable structure is known. Both structures show {sub {infinity}}{sup 1}[(CO{sub 3}{sup 2-})(H{sub 2}O)]-chains, being connected via additional H{sub 2}O forming columns (Rb{sub 2}CO{sub 3} . 1.5 H{sub 2}O) and layers (Cs{sub 2}CO{sub 3} . 3 H{sub 2}O), respectively. (orig.)

  13. The origin of the RB1 imprint.

    Deniz Kanber

    Full Text Available The human RB1 gene is imprinted due to a differentially methylated CpG island in intron 2. This CpG island is part of PPP1R26P1, a truncated retrocopy of PPP1R26, and serves as a promoter for an alternative RB1 transcript. We show here by in silico analyses that the parental PPP1R26 gene is present in the analysed members of Haplorrhini, which comprise Catarrhini (Old World Monkeys, Small apes, Great Apes and Human, Platyrrhini (New World Monkeys and tarsier, and Strepsirrhini (galago. Interestingly, we detected the retrocopy, PPP1R26P1, in all Anthropoidea (Catarrhini and Platyrrhini that we studied but not in tarsier or galago. Additional retrocopies are present in human and chimpanzee on chromosome 22, but their distinct composition indicates that they are the result of independent retrotransposition events. Chimpanzee and marmoset have further retrocopies on chromosome 8 and chromosome 4, respectively. To examine the origin of the RB1 imprint, we compared the methylation patterns of the parental PPP1R26 gene and its retrocopies in different primates (human, chimpanzee, orangutan, rhesus macaque, marmoset and galago. Methylation analysis by deep bisulfite sequencing showed that PPP1R26 is methylated whereas the retrocopy in RB1 intron 2 is differentially methylated in all primates studied. All other retrocopies are fully methylated, except for the additional retrocopy on marmoset chromosome 4, which is also differentially methylated. Using an informative SNP for the methylation analysis in marmoset, we could show that the differential methylation pattern of the retrocopy on chromosome 4 is allele-specific. We conclude that the epigenetic fate of a PPP1R26 retrocopy after integration depends on the DNA sequence and selective forces at the integration site.

  14. Chicken rRNA Gene Cluster Structure.

    Alexander G Dyomin

    Full Text Available Ribosomal RNA (rRNA genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5'ETS (1836 bp, 18S rRNA gene (1823 bp, ITS1 (2530 bp, 5.8S rRNA gene (157 bp, ITS2 (733 bp, 28S rRNA gene (4441 bp and 3'ETS (343 bp. The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region. The results have confirmed the chicken rRNA gene cluster validity.

  15. Generation of a Retinoblastoma (Rb)1-inducible dominant-negative (DN) mouse model.

    Tarang, Shikha; Doi, Songila M S R; Gurumurthy, Channabasavaiah B; Harms, Donald; Quadros, Rolen; Rocha-Sanchez, Sonia M


    Retinoblastoma 1 (Rb1) is an essential gene regulating cellular proliferation, differentiation, and homeostasis. To exert these functions, Rb1 is recruited and physically interacts with a growing variety of signaling pathways. While Rb1 does not appear to be ubiquitously expressed, its expression has been confirmed in a variety of hematopoietic and neuronal-derived cells, including the inner ear hair cells (HCs). Studies in transgenic mice demonstrate that complete germline or conditional Rb1 deletion leads to abnormal cell proliferation, followed by massive apoptosis; making it difficult to fully address Rb1's biochemical activities. To overcome these limitations, we developed a tetracycline-inducible TetO-CB-myc6-Rb1 (CBRb) mouse model to achieve transient and inducible dominant-negative (DN) inhibition of the endogenous RB1 protein. Our strategy involved fusing the Rb1 gene to the lysosomal protease pre-procathepsin B (CB), thus allowing for further routing of the DN-CBRb fusion protein and its interacting complexes for proteolytic degradation. Moreover, reversibility of the system is achieved upon suppression of doxycycline (Dox) administration. Preliminary characterization of DN-CBRb mice bred to a ubiquitous rtTA mouse line demonstrated a significant inhibition of the endogenous RB1 protein in the inner ear and in a number of other organs where RB1 is expressed. Examination of the postnatal (P) DN-CBRb mice inner ear at P10 and P28 showed the presence of supernumerary inner HCs (IHCs) in the lower turns of the cochleae, which corresponds to the described expression domain of the endogenous Rb1 gene. Selective and reversible suppression of gene expression is both an experimental tool for defining function and a potential means to medical therapy. Given the limitations associated with Rb1-null mice lethality, this model provides a valuable resource for understanding RB1 activity, relative contribution to HC regeneration and its potential therapeutic application.

  16. Lung neuroendocrine tumours: deep sequencing of the four World Health Organization histotypes reveals chromatin-remodelling genes as major players and a prognostic role for TERT, RB1, MEN1 and KMT2D.

    Simbolo, Michele; Mafficini, Andrea; Sikora, Katarzyna O; Fassan, Matteo; Barbi, Stefano; Corbo, Vincenzo; Mastracci, Luca; Rusev, Borislav; Grillo, Federica; Vicentini, Caterina; Ferrara, Roberto; Pilotto, Sara; Davini, Federico; Pelosi, Giuseppe; Lawlor, Rita T; Chilosi, Marco; Tortora, Giampaolo; Bria, Emilio; Fontanini, Gabriella; Volante, Marco; Scarpa, Aldo


    Next-generation sequencing (NGS) was applied to 148 lung neuroendocrine tumours (LNETs) comprising the four World Health Organization classification categories: 53 typical carcinoid (TCs), 35 atypical carcinoid (ACs), 27 large-cell neuroendocrine carcinomas, and 33 small-cell lung carcinomas. A discovery screen was conducted on 46 samples by the use of whole-exome sequencing and high-coverage targeted sequencing of 418 genes. Eighty-eight recurrently mutated genes from both the discovery screen and current literature were verified in the 46 cases of the discovery screen, and validated on additional 102 LNETs by targeted NGS; their prevalence was then evaluated on the whole series. Thirteen of these 88 genes were also evaluated for copy number alterations (CNAs). Carcinoids and carcinomas shared most of the altered genes but with different prevalence rates. When mutations and copy number changes were combined, MEN1 alterations were almost exclusive to carcinoids, whereas alterations of TP53 and RB1 cell cycle regulation genes and PI3K/AKT/mTOR pathway genes were significantly enriched in carcinomas. Conversely, mutations in chromatin-remodelling genes, including those encoding histone modifiers and members of SWI-SNF complexes, were found at similar rates in carcinoids (45.5%) and carcinomas (55.0%), suggesting a major role in LNET pathogenesis. One AC and one TC showed a hypermutated profile associated with a POLQ damaging mutation. There were fewer CNAs in carcinoids than in carcinomas; however ACs showed a hybrid pattern, whereby gains of TERT, SDHA, RICTOR, PIK3CA, MYCL and SRC were found at rates similar to those in carcinomas, whereas the MEN1 loss rate mirrored that of TCs. Multivariate survival analysis revealed RB1 mutation (p = 0.0005) and TERT copy gain (p = 0.016) as independent predictors of poorer prognosis. MEN1 mutation was associated with poor prognosis in AC (p = 0.0045), whereas KMT2D mutation correlated with longer survival in SCLC

  17. Deletion of Rb1 induces both hyperproliferation and cell death in murine germinal center B cells.

    He, Zhiwen; O'Neal, Julie; Wilson, William C; Mahajan, Nitin; Luo, Jun; Wang, Yinan; Su, Mack Y; Lu, Lan; Skeath, James B; Bhattacharya, Deepta; Tomasson, Michael H


    The retinoblastoma gene (RB1) has been implicated as a tumor suppressor in multiple myeloma (MM), yet its role remains unclear because in the majority of cases with 13q14 deletions, un-mutated RB1 remains expressed from the retained allele. To explore the role of Rb1 in MM, we examined the functional consequences of single- and double-copy Rb1 loss in germinal center B cells, the cells of origin of MM. We generated mice without Rb1 function in germinal center B cells by crossing Rb1(Flox/Flox) with C-γ-1-Cre (Cγ1) mice expressing the Cre recombinase in class-switched B cells in a p107(-/-) background to prevent p107 from compensating for Rb1 loss (Cγ1-Rb1(F/F)-p107(-/-)). All mice developed normally, but B cells with two copies of Rb1 deleted (Cγ1-Rb1(F/F)-p107(-/-)) exhibited increased proliferation and cell death compared with Cγ1-Rb1(+/+)-p107(-/-) controls ex vivo. In vivo, Cγ1-Rb1(F/F)-p107(-/-) mice had a lower percentage of splenic B220+ cells and reduced numbers of bone marrow antigen-specific secreting cells compared with control mice. Our data indicate that Rb1 loss induces both cell proliferation and death in germinal center B cells. Because no B-cell malignancies developed after 1 year of observation, our data also suggest that Rb1 loss is not sufficient to transform post-germinal center B cells and that additional, specific mutations are likely required to cooperate with Rb1 loss to induce malignant transformation.

  18. Silencing of RB1 and RB2/P130 during adipogenesis of bone marrow stromal cells results in dysregulated differentiation.

    Capasso, Stefania; Alessio, Nicola; Di Bernardo, Giovanni; Cipollaro, Marilena; Melone, Mariarosa Ab; Peluso, Gianfranco; Giordano, Antonio; Galderisi, Umberto


    Bone marrow adipose tissue (BMAT) is different from fat found elsewhere in the body, and only recently have some of its functions been investigated. BMAT may regulate bone marrow stem cell niche and plays a role in energy storage and thermogenesis. BMAT may be involved also in obesity and osteoporosis onset. Given the paramount functions of BMAT, we decided to better clarify the human bone marrow adipogenesis by analyzing the role of the retinoblastoma gene family, which are key players in cell cycle regulation. Our data provide evidence that the inactivation of RB1 or RB2/P130 in uncommitted bone marrow stromal cells (BMSC) facilitates the first steps of adipogenesis. In cultures with silenced RB1 or RB2/P130, we observed an increase of clones with adipogenic potential and a higher percentage of cells accumulating lipid droplets. Nevertheless, the absence of RB1 or RB2/P130 impaired the terminal adipocyte differentiation and gave rise to dysregulated adipose cells, with alteration in lipid uptake and release. For the first time, we evidenced that RB2/P130 plays a role in bone marrow adipogenesis. Our data suggest that while the inactivation of retinoblastoma proteins may delay the onset of last cell division and allow more BMSC to be committed to adipocyte, it did not allow a permanent cell cycle exit, which is a prerequisite for adipocyte terminal maturation.

  19. Genetic Predisposition to Retinoblastoma (Rb)


    Determination of 8 cytogenetic indicators in 14 cases of Rb,their 21 parents and 14 normal controls revealed various degrees ofchromosome instability and nondisjunction in the patients and their parents,indicating the presence of genetic neoplastic predisposition to neoplasm inRb patients.Eye Science 1993;9:149-152.

  20. Vaccination of elk (Cervus canadensis with Brucella abortus strain RB51 overexpressing superoxide dismutase and glycosyltransferase genes does not induce adequate protection against experimental Brucella abortus challenge

    Pauline eNol


    Full Text Available In recent years, elk (Cervus canadensis have been implicated as the source of Brucella abortus infection for numerous cattle herds in the Greater Yellowstone Area. In the face of environmental and ecological changes on the landscape, the range of infected elk is expanding. Consequently, the development of effective disease management strategies for wild elk herds is of utmost importance, not only for the prevention of reintroduction of brucellosis to cattle, but also for the overall health of the Greater Yellowstone Area elk populations. In two studies, we evaluated the efficacy of B. abortus strain RB51 over-expressing superoxide dismutase and glycosytransferase for protecting elk from infection and disease caused by B. abortus after experimental infection with a virulent B. abortus strain. Our data indicate that the recombinant vaccine does not protect elk against brucellosis. Further work is needed for development of an effective brucellosis vaccine for use in elk

  1. Vaccination of Elk (Cervus canadensis) with Brucella abortus Strain RB51 Overexpressing Superoxide Dismutase and Glycosyltransferase Genes Does Not Induce Adequate Protection against Experimental Brucella abortus Challenge.

    Nol, Pauline; Olsen, Steven C; Rhyan, Jack C; Sriranganathan, Nammalwar; McCollum, Matthew P; Hennager, Steven G; Pavuk, Alana A; Sprino, Phillip J; Boyle, Stephen M; Berrier, Randall J; Salman, Mo D


    In recent years, elk (Cervus canadensis) have been implicated as the source of Brucella abortus infection for numerous cattle herds in the Greater Yellowstone Area. In the face of environmental and ecological changes on the landscape, the range of infected elk is expanding. Consequently, the development of effective disease management strategies for wild elk herds is of utmost importance, not only for the prevention of reintroduction of brucellosis to cattle, but also for the overall health of the Greater Yellowstone Area elk populations. In two studies, we evaluated the efficacy of B. abortus strain RB51 over-expressing superoxide dismutase and glycosyltransferase for protecting elk from infection and disease caused by B. abortus after experimental infection with a virulent B. abortus strain. Our data indicate that the recombinant vaccine does not protect elk against brucellosis. Further, work is needed for development of an effective brucellosis vaccine for use in elk.

  2. Gene expression of the p16(INK4a)-Rb and p19(Arf)-p53-p21(Cip/Waf1) signaling pathways in the regulation of hematopoietic stem cell aging by ginsenoside Rg1.

    Yue, Z; Rong, J; Ping, W; Bing, Y; Xin, Y; Feng, L D; Yaping, W


    The elucidation of the molecular mechanisms underlying the effects of traditional Chinese medicines in clinical practice is a key step toward their worldwide application, and this topic is currently a subject of intense research interest. Rg1, a component of ginsenoside, has recently been shown to perform several pharmacological functions; however, the underlying mechanisms of these effects remain unclear. In the present study, we investigated whether Rg1 has an anti-senescence effect on hematopoietic stem cells (HSCs) and the possible molecular mechanisms driving any effects. The results showed that Rg1 could effectively delay tert-butyl hydroperoxide (t-BHP)-induced senescence and inhibit gene expression in the p16(INK4a)-Rb and p19(Arf)-p53-p21(Cip/Waf1) signaling pathways in HSCs. Our study suggested that these two signaling pathways might be potential targets for elucidating the molecular mechanisms of the Rg1 anti-senescence effect.

  3. Structure, expression and functions of MTA genes.

    Kumar, Rakesh; Wang, Rui-An


    Metastatic associated proteins (MTA) are integrators of upstream regulatory signals with the ability to act as master coregulators for modifying gene transcriptional activity. The MTA family includes three genes and multiple alternatively spliced variants. The MTA proteins neither have their own enzymatic activity nor have been shown to directly interact with DNA. However, MTA proteins interact with a variety of chromatin remodeling factors and complexes with enzymatic activities for modulating the plasticity of nucleosomes, leading to the repression or derepression of target genes or other extra-nuclear and nucleosome remodeling and histone deacetylase (NuRD)-complex independent activities. The functions of MTA family members are driven by the steady state levels and subcellular localization of MTA proteins, the dynamic nature of modifying signals and enzymes, the structural features and post-translational modification of protein domains, interactions with binding proteins, and the nature of the engaged and resulting features of nucleosomes in the proximity of target genes. In general, MTA1 and MTA2 are the most upregulated genes in human cancer and correlate well with aggressive phenotypes, therapeutic resistance, poor prognosis and ultimately, unfavorable survival of cancer patients. Here we will discuss the structure, expression and functions of the MTA family of genes in the context of cancer cells.

  4. The RB/E2F pathway and regulation of RNA processing

    Ahlander, Joseph [Department of Molecular and Cellular Biology, 1007 East Lowell Street, University of Arizona, Tucson, AZ 85721 (United States); Bosco, Giovanni, E-mail: [Department of Molecular and Cellular Biology, 1007 East Lowell Street, University of Arizona, Tucson, AZ 85721 (United States)


    The retinoblastoma tumor suppressor protein (RB) is inactivated in a majority of cancers. RB restricts cell proliferation by inhibiting the E2F family of transcription factors. The current model for RB/E2F function describes its role in regulating transcription at gene promoters. Whether the RB or E2F proteins might play a role in gene expression beyond transcription initiation is not well known. This review describes evidence that points to a novel role for the RB/E2F network in the regulation of RNA processing, and we propose a model as a framework for future research. The elucidation of a novel role of RB in RNA processing will have a profound impact on our understanding of the role of this tumor suppressor family in cell and developmental biology.

  5. Characterization and retinal neuron differentiation of WERI-Rb1 cancer stem cells

    Hu, Huiling; Deng, Fei; Liu, Ying; Chen, Mengfei; Zhang, Xiulan; Sun, Xuerong; Dong, Zhizhang; Xiaohong LIU; Ge, Jian


    Purpose The evidence is increasing that cancer stem cells (CSCs) expressing embryonic and neuronal stem cell markers are present in human retinoblastoma (Rb). This study was conducted to determine whether stem-like cancer cells (SLCCs) in Rb express retinal stem cell–related genes and whether SLCCs can directly differentiate into retinal neurons. Methods The cancer stem cell characteristics in WERI-Rb1 cells were determined with Hoechst 33,342 staining, clone formation assay, and CD133 flow c...

  6. RB loss contributes to aggressive tumor phenotypes in MYC-driven triple negative breast cancer.

    Knudsen, Erik S; McClendon, A Kathleen; Franco, Jorge; Ertel, Adam; Fortina, Paolo; Witkiewicz, Agnieszka K


    Triple negative breast cancer (TNBC) is characterized by multiple genetic events occurring in concert to drive pathogenic features of the disease. Here we interrogated the coordinate impact of p53, RB, and MYC in a genetic model of TNBC, in parallel with the analysis of clinical specimens. Primary mouse mammary epithelial cells (mMEC) with defined genetic features were used to delineate the combined action of RB and/or p53 in the genesis of TNBC. In this context, the deletion of either RB or p53 alone and in combination increased the proliferation of mMEC; however, the cells did not have the capacity to invade in matrigel. Gene expression profiling revealed that loss of each tumor suppressor has effects related to proliferation, but RB loss in particular leads to alterations in gene expression associated with the epithelial-to-mesenchymal transition. The overexpression of MYC in combination with p53 loss or combined RB/p53 loss drove rapid cell growth. While the effects of MYC overexpression had a dominant impact on gene expression, loss of RB further enhanced the deregulation of a gene expression signature associated with invasion. Specific RB loss lead to enhanced invasion in boyden chambers assays and gave rise to tumors with minimal epithelial characteristics relative to RB-proficient models. Therapeutic screening revealed that RB-deficient cells were particularly resistant to agents targeting PI3K and MEK pathway. Consistent with the aggressive behavior of the preclinical models of MYC overexpression and RB loss, human TNBC tumors that express high levels of MYC and are devoid of RB have a particularly poor outcome. Together these results underscore the potency of tumor suppressor pathways in specifying the biology of breast cancer. Further, they demonstrate that MYC overexpression in concert with RB can promote a particularly aggressive form of TNBC.

  7. Amplification and characterization of eukaryotic structural genes.

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F


    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  8. In vitro phosphorylation and acetylation of the murine pocket protein Rb2/p130.

    Muhammad Saeed

    Full Text Available The retinoblastoma protein (pRb and the related proteins Rb2/p130 and 107 represent the "pocket protein" family of cell cycle regulators. A key function of these proteins is the cell cycle dependent modulation of E2F-regulated genes. The biological activity of these proteins is controlled by acetylation and phosphorylation in a cell cycle dependent manner. In this study we attempted to investigate the interdependence of acetylation and phosphorylation of Rb2/p130 in vitro. After having identified the acetyltransferase p300 among several acetyltransferases to be associated with Rb2/p130 during S-phase in NIH3T3 cells in vivo, we used this enzyme and the CDK4 protein kinase for in vitro modification of a variety of full length Rb2/p130 and truncated versions with mutations in the acetylatable lysine residues 1079, 128 and 130. Mutation of these residues results in the complete loss of Rb2/p130 acetylation. Replacement of lysines by arginines strongly inhibits phosphorylation of Rb2/p130 by CDK4; the inhibitory effect of replacement by glutamines is less pronounced. Preacetylation of Rb2/p130 strongly enhances CDK4-catalyzed phosphorylation, whereas deacetylation completely abolishes in vitro phosphorylation. In contrast, phosphorylation completely inhibits acetylation of Rb2/p130 by p300. These results suggest a mutual interdependence of modifications in a way that acetylation primes Rb2/p130 for phosphorylation and only dephosphorylated Rb2/p130 can be subject to acetylation. Human papillomavirus 16-E7 protein, which increases acetylation of Rb2/p130 by p300 strongly reduces phosphorylation of this protein by CDK4. This suggests that the balance between phosphorylation and acetylation of Rb2/p130 is essential for its biological function in cell cycle control.

  9. Rb1基因第24和25外显子缺失导致低外显性视网膜母细胞瘤%Low-penetrance retinoblastoma due to exons 24 and 25 deletions in the Rb1 gene

    杜琴; 江悦华; 等


    目的探讨抑癌基因Rb1大片段缺失与低外显性视网膜母细胞瘤(low-penetrance retinoblastoma)家系的相关性.方法应用定量多重PCR技术(quantitative fluorescent multiplex PCR, QFM-PCR)筛查Rb1突变.应用长片段聚合酶链反应(long fragment PCR)、逆转录聚合酶链反应(reverse transcriptase-PCR,RT-PCR)、亚克隆、直接测序、Western 印迹等技术分析Rb1突变点的特征.结果发现1个家族4代122人中,共有18人携带Rb1第24和25外显子缺失突变, 而这些高风险的Rb1突变基因携带者中,只有11人(39%)形成单眼或双眼视网膜母细胞瘤(retinoblastoma ,RB),比常见的Rb1基因突变者中有95%形成RB的发病率明显较低.该突变的缺失长达4 kb 基因组DNA. cDNA、RNA和测序研究证实,有174 bp碱基缺失导致58个密码子丢失.Western 印迹检测出一个比正常RB1蛋白短、相对分子质量6000(约6000Da)的RB突变蛋白得以表达. 结论应用QFM-PCR技术在一个RB呈低外显性的大家族中发现Rb1第24和25外显子完全缺失.该突变在基因组DNA、RNA和蛋白质水平的研究结果,为遗传性低外显性视网膜母细胞瘤与该段DNA缺失相关提供了新的依据,并为遗传咨询提供了有价值的资料.

  10. Ternary K2Zn5As4-type pnictides Rb2Cd5As4 and Rb2Zn5Sb4, and the solid solution Rb2Cd5(As,Sb)4.

    He, Hua; Stoyko, Stanislav S; Mar, Arthur; Bobev, Svilen


    Dirubidium pentacadmium tetraarsenide, Rb2Cd5As4, dirubidium pentazinc tetraantimonide, Rb2Zn5Sb4, and the solid-solution phase dirubidium pentacadmium tetra(arsenide/antimonide), Rb2Cd5(As,Sb)4 [or Rb2Cd5As3.00(1)Sb1.00(1)], have been prepared by direct reaction of the component elements at high temperature. These compounds are charge-balanced Zintl phases and adopt the orthorhombic K2Zn5As4-type structure (Pearson symbol oC44), featuring a three-dimensional [M5Pn4](2-) framework [M = Zn or Cd; Pn is a pnicogen or Group 15 (Group V) element] built of linked MPn4 tetrahedra, and large channels extending along the b axis which host Rb(+) cations. The As and Sb atoms in Rb2Cd5(As,Sb)4 are randomly disordered over the two available pnicogen sites. Band-structure calculations predict that Rb2Cd5As4 is a small-band-gap semiconductor and Rb2Zn5Sb4 is a semimetal.

  11. The Mycoplasma hominis vaa gene displays a mosaic gene structure

    Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.;


    Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular compos...

  12. Loss of heterozygosity for Rb locus and pRb immunostaining in laryngeal cancer: a clinicopathologic, molecular and immunohistochemical study.

    Andrzej Borzecki


    Full Text Available Several risk factors for the development of laryngeal cancer have been identified, such as smoking and alcohol consumption, but the molecular mechanisms related to the carcinogenesis in the larynx remain under investigation. In this context, deregulations of the cell-cycle-controling mechanisms, Rb-pathway in particular, have been suggested to be involved in the pathogenesis of laryngeal carcinoma. Our purpose was to investigate 13q14 LOH and the expression of Rb protein and their possible prognostic value in laryngeal cancer. The group of 67 patients with laryngeal cancer, surgically treated with minimum 5 years observation, was multi-variously analysed. LOH for Rb was investigated by PCR-based techniques using two microsatellite markers, D13S263 and D13S126, flanking the Rb locus. Amplification products from each polymorphism were fractionated by denaturing gel electrophoresis and detected by audioradiography. Immunohistochemical staining of paraffin specimens of laryngeal cancers was supervised by the use of monoclonal mouse antibodies IgG1 (Anti-Human Retinoblastoma Gene Product of Dako in dilution of 1:50. Inactivation of Rb protein was assumed to represent the expression in < or =10% tumour cells. The results of each examined individual factor were compared with clinicopathologic features and the results were statistically transformed (Chi-square test with Yates' correction, Mann-Whitney test. The Kaplan and Meier model was used for overall and disease free survival curves. Only p value of less than 0,05 was considered significant. 13q14 LOH was detected in 7/67 (10,4% of informative tumours. No correlations were found between Rb genetic alteration (LOH and gender, age, TNM staging, histological differentiation, nodal and local recurrences (p>0.05. There was a strong association between the loss of Rb and supraglottic localisation of tumour in the larynx (p<0.01. By univariate analysis 13q14 LOH proved to be significantly related to the

  13. pRB binds to and modulates the transrepressing activity of the E1A-regulated transcription factor p120E4F

    Fajas, L.; Paul, C.; Zugasti, O.; Cam, L. Le; Polanowska, J.; Fabbrizio, E.; Medema, R.H.; Vignais, M.-L.; Sardet, C.


    The retinoblastoma protein pRB is involved in the transcriptional control of genes essential for cell cycle progression and differentiation. pRB interacts with different transcription factors and thereby modulates their activity by sequestration, corepression, or activation. We report that pRB, but

  14. Irreversibility of cellular senescence: dual roles of p16INK4a/Rb-pathway in cell cycle control

    Hara Eiji


    Full Text Available Abstract The retinoblastoma (Rb tumor suppressor gene product, pRb, has an established role in the implementation of cellular senescence, the state of irreversible G1 cell cycle arrest provoked by diverse oncogenic stresses. In murine cells, senescence cell cycle arrest can be reversed by subsequent inactivation of pRb, indicating that pRb is required not only for the onset of cellular senescence, but also for the maintenance of senescence program in murine cells. However, in human cells, once pRb is fully activated by p16INK4a, senescence cell cycle arrest becomes irreversible and is no longer revoked by subsequent inactivation of pRb, suggesting that p16INK4a/Rb-pathway activates an alternative mechanism to irreversibly block the cell cycle in human senescent cells. Here, we discuss the molecular mechanism underlying the irreversibility of senescence cell cycle arrest and its potential towards tumor suppression.

  15. Melanin Biosynthesis Inhibition Effects of Ginsenoside Rb2 Isolated from Panax ginseng Berry.

    Lee, Dae Young; Jeong, Yong Tae; Jeong, Sang Chul; Lee, Mi Kyoung; Min, Jin Woo; Lee, Jae Won; Kim, Geum Soog; Lee, Seung Eun; Ahn, Young Sup; Kang, Hee Cheol; Kim, Jin Hee


    Ginsenoside Rb2 (Gin-Rb2) was purified from the fruit extract of Panax ginseng. Its chemical structure was measured by spectroscopic analysis, including HR-FAB-MS, (1)H-NMR, and IR spectroscopy. Gin-Rb2 decreased potent melanogenesis in melan-a cells, with 23.4% at 80 μM without cytotoxicity. Gin-Rb2 also decreased tyrosinase and MITF protein expression in melan-a cells. Furthermore, Gin-Rb2 presented inhibition of the body pigmentation in the zebrafish in vivo system and reduced melanin contents and tyrosinase activity. These results show that Gin-Rb2 isolated from P. ginseng may be an effective skin-whitening agent via the in vitro and in vivo systems.

  16. p21 suppresses inflammation and tumorigenesis on pRB-deficient stratified epithelia.

    Saiz-Ladera, C; Lara, M F; Garín, M; Ruiz, S; Santos, M; Lorz, C; García-Escudero, R; Martínez-Fernández, M; Bravo, A; Fernández-Capetillo, O; Segrelles, C; Paramio, J M


    The retinoblastoma gene product (pRb) controls proliferation and differentiation processes in stratified epithelia. Importantly, and in contrast to other tissues, Rb deficiency does not lead to spontaneous skin tumor formation. As the cyclin-dependent kinase inhibitor p21 regulates proliferation and differentiation in the absence of pRb, we analyzed the consequences of deleting p21 in pRb-ablated stratified epithelia (hereafter pRb(ΔEpi);p21-/-). These mice display an enhancement of the phenotypic abnormalities observed in pRb(ΔEpi) animals, indicating that p21 partially compensates pRb absence. Remarkably, pRb(ΔEpi);p21-/- mice show an acute skin inflammatory phenotype and develop spontaneous epithelial tumors, particularly affecting tongue and oral tissues. Biochemical analyses and transcriptome studies reveal changes affecting multiple pathways, including DNA damage and p53-dependent signaling responses. Comparative metagenomic analyses, together with the histopathological profiles, indicate that these mice constitute a faithful model for human head and neck squamous cell carcinomas. Collectively, our findings demonstrate that p21, in conjunction with pRb, has a central role in regulating multiple epithelial processes and orchestrating specific tumor suppressor functions.

  17. Inhibition of pRB Pathway Differentially Modulates Apoptosis in Esophageal Cancer Cells.

    Soletti, Rossana C; Biasoli, Deborah; Rodrigues, Nathassya A L V; Delou, João M A; Maciel, Renata; Chagas, Vera L A; Martins, Rodrigo A P; Rehen, Stevens K; Borges, Helena L


    Esophageal cancer is the sixth most common cause of cancer-related death worldwide. Current chemotherapy regimens include a combination of 5-fluorouracil (5-FU) and cisplatin, but more efficient therapy strategies are needed to increase 5-year survival. Alterations in the signaling pathway of the tumor suppressor gene Rb-1, which encodes a phosphoprotein (pRB) that negatively regulates the G1/S transition of the cell cycle, are present in 70% of all tumors, but its role in esophageal cancer is still unclear. Most of these are alterations leading to up-regulation of the activity of cyclin-dependent kinases (CDKs) to phosphorylate pRB, which suggests that keeping the wild type pRB phosphorylated might be advantageous. Besides proliferation, pRB also regulates apoptosis induced by tumor necrosis factor-alpha (TNF-α) and DNA-damage. We investigated the status of phosphorylation of pRB along esophageal tumorigenesis stages, as well as whether hyperphosphorylation of pRB could suppress apoptosis induced by cisplatin, 5-FU, or TNF-α in esophageal cancer cells. pRB phosphorylation increased progressively from normal esophageal tissue to metaplasia and adenocarcinoma, suggesting that pRB phosphorylation increases along esophageal tumor stages. When RB-1 was knocked down or CDK inhibitors reduced the levels of phosphorylated pRB, opposite apoptotic effects were observed, depending on the combination of drugs tested: whereas TNF-α- and cisplatin-induced apoptosis increased, 5-FU-induced apoptosis decreased. Taken together, these data suggest that pRB plays a role in esophageal adenocarcinoma and that, depending on the type of anti-cancer treatment, combining CDK inhibitors and chemotherapy has the potential to increase the sensitivity of esophageal cancer cells to cell death. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  18. A kinase shRNA screen links LATS2 and the pRB tumor suppressor.

    Tschöp, Katrin; Conery, Andrew R; Litovchick, Larisa; Decaprio, James A; Settleman, Jeffrey; Harlow, Ed; Dyson, Nicholas


    pRB-mediated inhibition of cell proliferation is a complex process that depends on the action of many proteins. However, little is known about the specific pathways that cooperate with the Retinoblastoma protein (pRB) and the variables that influence pRB's ability to arrest tumor cells. Here we describe two shRNA screens that identify kinases that are important for pRB to suppress cell proliferation and pRB-mediated induction of senescence markers. The results reveal an unexpected effect of LATS2, a component of the Hippo pathway, on pRB-induced phenotypes. Partial knockdown of LATS2 strongly suppresses some pRB-induced senescence markers. Further analysis shows that LATS2 cooperates with pRB to promote the silencing of E2F target genes, and that reduced levels of LATS2 lead to defects in the assembly of DREAM (DP, RB [retinoblastoma], E2F, and MuvB) repressor complexes at E2F-regulated promoters. Kinase assays show that LATS2 can phosphorylate DYRK1A, and that it enhances the ability of DYRK1A to phosphorylate the DREAM subunit LIN52. Intriguingly, the LATS2 locus is physically linked with RB1 on 13q, and this region frequently displays loss of heterozygosity in human cancers. Our results reveal a functional connection between the pRB and Hippo tumor suppressor pathways, and suggest that low levels of LATS2 may undermine the ability of pRB to induce a permanent cell cycle arrest in tumor cells.

  19. Syntheses, structure and intercalation properties of low-dimensional phenylarsonates, A(HO3AsC6H5)(H2O3AsC6H5) (A = Tl, Na, K and Rb)

    Bonthu Krishna Kishore Reddy; K Prabhakara Rao; K Vidyasagar


    Four new low-dimensional phenylarsonates, A(HO3AsC6H5)(H2O3AsC6H5) (A = Tl(1), Na(2), K(3) and Rb(4)), have been synthesized and characterized by X-ray diffraction, spectroscopic and thermal studies. They crystallize in triclinic unit cells and have approximately planar arrangement of A+ ions, coordinated to oxygen atoms of phenylarsonates, on both sides. Structure of thallium phenylarsonate as determined by single crystal X-ray diffraction, is one-dimensional, whereas those of alkalimetal analogues are two-dimensional. Successful intercalation reactions of compounds 1 and 2 with primary -alkyl amines have been demonstrated.

  20. Optical, Structural and Paramagnetic Properties of Eu-Doped Ternary Sulfides ALnS2 (A = Na, K, Rb; Ln = La, Gd, Lu, Y

    Vítězslav Jarý


    Full Text Available Eu-doped ternary sulfides of general formula ALnS2 (A = Na, K, Rb; Ln = La, Gd, Lu, Y are presented as a novel interesting material family which may find usage as X-ray phosphors or solid state white light emitting diode (LED lighting. Samples were synthesized in the form of transparent crystalline hexagonal platelets by chemical reaction under the flow of hydrogen sulfide. Their physical properties were investigated by means of X-ray diffraction, time-resolved photoluminescence spectroscopy, electron paramagnetic resonance, and X-ray excited fluorescence. Corresponding characteristics, including absorption, radioluminescence, photoluminescence excitation and emission spectra, and decay kinetics curves, were measured and evaluated in a broad temperature range (8–800 K. Calculations including quantum local crystal field potential and spin-Hamiltonian for a paramagnetic particle in D3d local symmetry and phenomenological model dealing with excited state dynamics were performed to explain the experimentally observed features. Based on the results, an energy diagram of lanthanide energy levels in KLuS2 is proposed. Color model xy-coordinates are used to compare effects of dopants on the resulting spectrum. The application potential of the mentioned compounds in the field of white LED solid state lighting or X-ray phosphors is thoroughly discussed.

  1. pRb is an obesity suppressor in hypothalamus and high-fat diet inhibits pRb in this location.

    Lu, Zhonglei; Marcelin, Genevieve; Bauzon, Frederick; Wang, Hongbo; Fu, Hao; Dun, Siok Le; Zhao, Hongling; Li, Xiaosong; Jo, Young-Hwan; Wardlaw, Sharon; Dun, Nae; Chua, Streamson; Zhu, Liang


    pRb is frequently inactivated in tumours by mutations or phosphorylation. Here, we investigated whether pRb plays a role in obesity. The Arcuate nucleus (ARC) in hypothalamus contains antagonizing POMC and AGRP/NPY neurons for negative and positive energy balance, respectively. Various aspects of ARC neurons are affected in high-fat diet (HFD)-induced obesity mouse model. Using this model, we show that HFD, as well as pharmacological activation of AMPK, induces pRb phosphorylation and E2F target gene de-repression in ARC neurons. Some affected neurons express POMC; and deleting Rb1 in POMC neurons induces E2F target gene de-repression, cell-cycle re-entry, apoptosis, and a hyperphagia-obesity-diabetes syndrome. These defects can be corrected by combined deletion of E2f1. In contrast, deleting Rb1 in the antagonizing AGRP/NPY neurons shows no effects. Thus, pRb-E2F1 is an obesity suppression mechanism in ARC POMC neurons and HFD-AMPK inhibits this mechanism by phosphorylating pRb in this location.

  2. Structure and superconductivity of (Li1-x Fe x )OHFeSe single crystals grown using A x Fe2-y Se2 (A  =  K, Rb, and Cs) as precursors

    Yu, G.; Zhang, G. Y.; Ryu, G. H.; Lin, C. T.


    We present results on the hydrothermal growth of (\\text{L}{{\\text{i}}1-x}\\text{F}{{\\text{e}}x} )OHFeSe single crystals using floating-zone-grown {{A}x}\\text{F}{{\\text{e}}2-y}\\text{S}{{\\text{e}}2} (A  =  K, Rb, and Cs) as precursors. The growth proceeds by the hydrothermal ion exchange of Li/Fe-O-H for K, Rb, and Cs, resulting in a stacking layer of (\\text{L}{{\\text{i}}1-x}\\text{F}{{\\text{e}}x} )OH sandwiched between the FeSe layers. Optimal growth parameters are achieved using high quality A 0.80Fe1.81Se2 single crystals added to the mixtures of LiOH, H2O, Fe and C(NH2)2Se in an autoclave and subsequently heated to 120 °C for 2 d, to obtain highest quality single crystals. The obtained crystals have lateral dimensions up to centimeters, with the final size related to that of the precursor crystal used. All (\\text{L}{{\\text{i}}1-x}\\text{F}{{\\text{e}}x} )OHFeSe single crystals show a superconducting transition temperature T c  >  42 K, regardless of the phase of the precursor such as superconducting K0.80Fe1.81Se2 (T c  =  29.31 K) or non-superconducting Rb0.80Fe1.81Se2 or poor-superconducting Cs0.80Fe1.81Se2 (T c  =  28.67 K). The T c and transition width ΔT vary in the obtained single crystals, due to the inhomogeneity of the ionic exchange. X-ray diffraction analysis demonstrates that the 245 insulating phase is absent in the ion-exchanged single crystals, while it is observed in the {{A}x}\\text{F}{{\\text{e}}2-y}\\text{S}{{\\text{e}}2} precursors. Comparative studies of the structure, magnetization, and superconductivity on the parent A 0.80Fe1.81Se2 and the ion-exchanged (\\text{L}{{\\text{i}}1-x}\\text{F}{{\\text{e}}x} )OHFeSe crystals are discussed. A phase diagram including antiferromagnetic spin density wave and superconducting phases is also proposed.

  3. The ancient function of RB-E2F Pathway: insights from its evolutionary history

    Yang Xianmei


    Full Text Available Abstract Background The RB-E2F pathway is conserved in most eukaryotic lineages, including animals and plants. E2F and RB family proteins perform crucial functions in cycle controlling, differentiation, development and apoptosis. However, there are two kinds of E2Fs (repressive E2Fs and active E2Fs and three RB family members in human. Till now, the detail evolutionary history of these protein families and how RB-E2F pathway evolved in different organisms remain poorly explored. Results We performed a comprehensive evolutionary analysis of E2F, RB and DP (dimerization partners of E2Fs protein family in representative eukaryotic organisms. Several interesting facts were revealed. First, orthologues of RB, E2F, and DP family are present in several representative unicellular organisms and all multicellular organisms we checked. Second, ancestral E2F, RB genes duplicated before placozoans and bilaterians diverged, thus E2F family was divided into E2F4/5 subgroup (including repressive E2Fs: E2F4 and E2F5 and E2F1/2/3 subgroup (including active E2Fs: E2F1, E2F2 and E2F3, RB family was divided into RB1 subgroup (including RB1 and RBL subgroup (including RBL1 and RBL2. Third, E2F4 and E2F5 share more sequence similarity with the predicted E2F ancestral sequence than E2F1, E2F2 and E2F3; E2F4 and E2F5 also possess lower evolutionary rates and higher purification selection pressures than E2F1, E2F2 and E2F3. Fourth, for RB family, the RBL subgroup proteins possess lower evolutionary rates and higher purification selection pressures compared with RB subgroup proteins in vertebrates, Conclusions Protein evolutionary rates and purification selection pressures are usually linked with protein functions. We speculated that function conducted by E2F4/5 subgroup and RBL subgroup proteins might mainly represent the ancient function of RB-E2F pathway, and the E2F1/2/3 subgroup proteins and RB1 protein might contribute more to functional diversification in RB-E2F

  4. The ancient function of RB-E2F pathway: insights from its evolutionary history.

    Cao, Lihuan; Peng, Bo; Yao, Lei; Zhang, Xinming; Sun, Kuan; Yang, Xianmei; Yu, Long


    The RB-E2F pathway is conserved in most eukaryotic lineages, including animals and plants. E2F and RB family proteins perform crucial functions in cycle controlling, differentiation, development and apoptosis. However, there are two kinds of E2Fs (repressive E2Fs and active E2Fs) and three RB family members in human. Till now, the detail evolutionary history of these protein families and how RB-E2F pathway evolved in different organisms remain poorly explored. We performed a comprehensive evolutionary analysis of E2F, RB and DP (dimerization partners of E2Fs) protein family in representative eukaryotic organisms. Several interesting facts were revealed. First, orthologues of RB, E2F, and DP family are present in several representative unicellular organisms and all multicellular organisms we checked. Second, ancestral E2F, RB genes duplicated before placozoans and bilaterians diverged, thus E2F family was divided into E2F4/5 subgroup (including repressive E2Fs: E2F4 and E2F5) and E2F1/2/3 subgroup (including active E2Fs: E2F1, E2F2 and E2F3), RB family was divided into RB1 subgroup (including RB1) and RBL subgroup (including RBL1 and RBL2). Third, E2F4 and E2F5 share more sequence similarity with the predicted E2F ancestral sequence than E2F1, E2F2 and E2F3; E2F4 and E2F5 also possess lower evolutionary rates and higher purification selection pressures than E2F1, E2F2 and E2F3. Fourth, for RB family, the RBL subgroup proteins possess lower evolutionary rates and higher purification selection pressures compared with RB subgroup proteins in vertebrates, Protein evolutionary rates and purification selection pressures are usually linked with protein functions. We speculated that function conducted by E2F4/5 subgroup and RBL subgroup proteins might mainly represent the ancient function of RB-E2F pathway, and the E2F1/2/3 subgroup proteins and RB1 protein might contribute more to functional diversification in RB-E2F pathway. Our results will enhance the current

  5. Hydrothermal Synthesis of RbLn2F7 and VUV Spectroscopy of RbLn2F7:Eu3+(Ln=Gd, Y)


    RbLn2F7 (Ln=Gd, Y, Er, Yb and Lu), crystallized in the hexagonal RbEr2F7 structure type, is synthesized by a hydrothermal method. The excitation spectra of Eu3+-doped RbGd(Y)2F7 suggest that the oxygen content is very low in the samples obtained by hydrothermal synthesis. Only the f-f transitions of Gd3+ ions are observed in the excitation spectrum of RbGd2F7:Eu3+ (0.5mol%), while those of Eu3+ ions do not appear. When the Gd3+ ions are excited, the absorbed energy is transferred efficiently from Gd3+ to Eu3+. The spectra show that the doped Eu3+ ions are located in non-centrosymmetric sites in hexagonal RbLn2F7.

  6. Spectroscopy of ultracold LiRb molecules using ionization detection

    Altaf, Adeel

    We present spectroscopic studies of ultracold LiRb molecules using ionization detection. The molecules are created by cooling and trapping Li and Rb atoms in overlapping magneto-optical traps (MOTs) and using light resonant with a free-bound transition to create weakly bound excited state molecules in a process known as photoassociation (PA). We explore weakly bound vibrational levels of LiRb with PA spectroscopy using ionization detection and, where possible, compare our results with earlier measurements performed in our lab using trap-loss spectroscopy. In addition, we also probe vibrational levels of the ground triplet electronic state and excited electronic states using resonantly enhanced multiphoton ionization (REMPI) spectroscopy. We identify several vibrational levels of the alpha3Sigma+, (3)3piO and (4)3Sigma + states and compare our observations with theoretical calculations. As LiRb is one of the least studied heteronuclear diatomic molecules, these studies are aimed towards exploring the molecular structure. The spectroscopic work is also in line with the long-term project goals of transferring ultracold LiRb molecules into the lowest rotational and vibrational levels of the ground singlet electronic state. Molecules in this rovibronic ground state possess a large electric dipole moment, which is essential for application of ultracold molecules in various quantum computation schemes. The rovibronic ground state will also be an ideal starting point for investigating molecular entangled states.

  7. Ginsenoside Rb1 attenuates activated microglia-induced neuronal damage

    Lining Ke; Wei Guo; Jianwen Xu; Guodong Zhang; Wei Wang; Wenhua Huang


    The microglia-mediated inlfammatory reaction promotes neuronal damage under cerebral isch-emia/hypoxia conditions. We therefore speculated that inhibition of hypoxia-induced microglial activation may alleviate neuronal damage. To test this hypothesis, we co-cultured ginsenoside Rb1, an active component of ginseng, and cortical neurons. Ginsenoside Rb1 protected neuronal morphology and structure in a single hypoxic culture system and in a hypoxic co-culture system with microglia, and reduced neuronal apoptosis and caspase-3 production. The protective effect was observable prior to placing in co-culture. Additionally, ginsenoside Rb1 inhibited levels of tumor necrosis factor-αin a co-culture system containing activated N9 microglial cells. Ginse-noside Rb1 also signiifcantly decreased nitric oxide and superoxide production induced by N9 microglia. Our ifndings indicate that ginsenoside Rb1 attenuates damage to cerebral cortex neu-rons by downregulation of nitric oxide, superoxide, and tumor necrosis factor-αexpression in hypoxia-activated microglia.

  8. TNFα modulates Fibroblast Growth Factor Receptor 2 gene expression through the pRB/E2F1 pathway: identification of a non-canonical E2F binding motif.

    Sirio D'Amici

    Full Text Available Interactions between epithelium and mesenchyme during wound healing are not fully understood, but Fibroblast Growth Factors (FGFs and their receptors FGFRs are recognized as key elements. FGFR2 gene encodes for two splicing transcript variants, FGFR2-IIIb or Keratinocyte Growth Factor Receptor (KGFR and FGFR2-IIIc, which differ for tissue localization and ligand specificity. Proinflammatory cytokines play an essential role in the regulation of epithelial-mesenchymal interactions, and have been indicated to stimulate FGFs production. Here we demonstrated that upregulation of FGFR2 mRNA and protein expression is induced by the proinflammatory cytokines Tumor Necrosis Factor-α, Interleukin-1β and Interleukin 2. Furthermore, we found that TNFα determines FGFR2 transcriptional induction through activation of pRb, mediated by Raf and/or p38 pathways, and subsequent release of the transcription factor E2F1. Experiments based on FGFR2 promoter serial deletions and site-directed mutagenesis allowed us to identify a minimal responsive element that retains the capacity to be activated by E2F1. Computational analysis indicated that this element is a non-canonical E2F responsive motif. Thus far, the molecular mechanisms of FGFR2 upregulation during wound healing or in pathological events are not known. Our data suggest that FGFR2 expression can be modulated by local recruitment of inflammatory cytokines. Furthermore, since alterations in FGFR2 expression have been linked to the pathogenesis of certain human cancers, these findings could also provide elements for diagnosis and potential targets for novel therapeutic approaches.

  9. Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell.

    Li, Dong; Sun, Hui; Sun, Wen-Jing; Bao, Hong-Bo; Si, Shu-Han; Fan, Jia-Lin; Lin, Ping; Cui, Rong-Jun; Pan, Yu-Jia; Wen, Si-Min; Zheng, Xiu-Lan; Yu, Xiao-Guang


    EMT (epithelial-mesenchymal transition) occurs in a wide range of tumor types, and has been shown to be crucial for metastasis. Epigenetic modifications of histones contribute to chromatin structure and result in the alterations in gene expression. Tri-methylation of histone H3 lysine 4 (H3K4me3) is associated with the promoters of actively transcribed genes and can serve as a transcriptional on/off switch. RbBP5 is a component of the COMPASS/ -like complex, which catalyzes H3K4me3 formation. In this study, we found that in the process of TGF-Beta1 induced EMT in the prostate cancer cell line DU145, H3K4me3 enrichment and RbBP5 binding increased in the vicinity of Snail (SNAI1) transcription start site. Knocking-down of RbBP5 notably decreased Snail expression and EMT. Recruitment of RbBP5 and formation of H3K4me3 at Snail TSS during EMT depend on binding of SMAD2/3 and CBP at Snail TSS. This study links the SMAD2/3 signal with Snail transcription via a histone modification - H3K4me3. Furthermore, our research also demonstrates that RbBP5 and even WRAD may be a promising therapeutic candidates in treating prostate cancer metastasis, and that DU145 cells maintain their incomplete mesenchymal state in an auto/ paracrine manner.

  10. RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation

    Jones, Robert A.; Robinson, Tyler J.; Liu, Jeff C.; Shrestha, Mariusz; Voisin, Veronique; Ju, YoungJun; Chung, Philip E.D.; Pellecchia, Giovanna; Fell, Victoria L.; Bae, SooIn; Muthuswamy, Lakshmi; Egan, Sean E.; Jiang, Zhe; Leone, Gustavo; Bader, Gary D.; Schimmer, Aaron


    Triple-negative breast cancer (TNBC) includes basal-like and claudin-low subtypes for which no specific treatment is currently available. Although the retinoblastoma tumor-suppressor gene (RB1) is frequently lost together with TP53 in TNBC, it is not directly targetable. There is thus great interest in identifying vulnerabilities downstream of RB1 that can be therapeutically exploited. Here, we determined that combined inactivation of murine Rb and p53 in diverse mammary epithelial cells induced claudin-low–like TNBC with Met, Birc2/3-Mmp13-Yap1, and Pvt1-Myc amplifications. Gene set enrichment analysis revealed that Rb/p53-deficient tumors showed elevated expression of the mitochondrial protein translation (MPT) gene pathway relative to tumors harboring p53 deletion alone. Accordingly, bioinformatic, functional, and biochemical analyses showed that RB1-E2F complexes bind to MPT gene promoters to regulate transcription and control MPT. Additionally, a screen of US Food and Drug Administration–approved (FDA-approved) drugs identified the MPT antagonist tigecycline (TIG) as a potent inhibitor of Rb/p53-deficient tumor cell proliferation. TIG preferentially suppressed RB1-deficient TNBC cell proliferation, targeted both the bulk and cancer stem cell fraction, and strongly attenuated xenograft growth. It also cooperated with sulfasalazine, an FDA-approved inhibitor of cystine xCT antiporter, in culture and xenograft assays. Our results suggest that RB1 deficiency promotes cancer cell proliferation in part by enhancing mitochondrial function and identify TIG as a clinically approved drug for RB1-deficient TNBC. PMID:27571409

  11. Intermediate-range chemical ordering of cations in molten RbCl-AgCl

    Tahara, S. [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, Okinawa 903-0213 (Japan); Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), Hyogo 679-5198 (Japan); Kawakita, Y. [J-PARC Center, Japan Atomic Energy Agency (JAEA), Ibaraki 319-1195 (Japan); Shimakura, H. [Faculty of Pharmacy, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603 (Japan); Ohara, K. [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), Hyogo 679-5198 (Japan); Fukami, T. [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, Okinawa 903-0213 (Japan); Takeda, S. [Department of Physics, Faculty of Sciences, Kyushu University, Fukuoka 812-8581 (Japan)


    A first sharp diffraction peak (FSDP) is observed in the X-ray total structure factor of a molten mixture of RbCl-AgCl, while both pure melts of RbCl and AgCl do not exhibit FSDP individually. Molecular dynamics simulations were performed to investigate the origin of the FSDP with the polarizable ion model (PIM). Coexistence of covalent Ag–Cl and ionic Rb–Cl bonds leads the system to evolve intermediate range ordering, which is simulated by introducing the induced polarization in different ways between Ag–Cl with fully polarizable treatment based on Vashishta-Raman potential and Rb–Cl with suppression over-polarization in the nearest neighbor contribution based on Born-Meyer potential. The partial structure factors for both the Ag–Ag and Rb–Rb correlations, S{sub AgAg}(Q) and S{sub RbRb}(Q), show a positive contribution to the FSDP, while S{sub AgRb}(Q) for the Ag–Rb correlation exhibits a negative contribution, indicating that Ag and Rb ions are distributed in an alternating manner within the intermediate-range length scale. The origin of the intermediate-range chemical ordering of cations can be ascribed to the preferred direction of the dipole moments of anions in the PIM.

  12. Genomic structure, characterization, and identification of the promotor of the human IL-8 receptor A gene

    Sprenger, H.; Lloyd, A.R.; Meyer, R.G.; Johnston, J.A.; Kelvin, D.J. [National Cancer Institute, Frederick, MA (United States)


    Two unique but homologous receptors for the neutrophil chemoattractant IL-8 have been cloned (designated IL-8RA and IL-8RB), each of which binds IL-8 with high affinity. IL-8RA mRNA expression was found to be regulated by granulocyte-CSF and LPS. In an attempt to understand the tissue-specific expression and to identify transcriptional regulatory elements, the authors have cloned, sequenced, and characterized the human IL-8RA gene. A {lambda}-DASH clone encoding the entire human IL-8RA gene was isolated by screening a genomic library with a PCR-generated cDNA. After mapping, subcloning, and sequencing several restriction fragments, a 9.2-kb continuous DNA sequence was obtained. As the sizes of the published cDNA (1.9 kb) and the mRNA determined by Northern blot analysis (2.1 kb) were not in agreement, a full-length cDNA was cloned by using a modified rapid amplification of cDNA ends technique. They identified a 5{prime}-untranslated region of 119 bp. After comparison with the genomic sequence, they found the gene consisted of two exons interrupted by an intron of 1.7 kb. A 1050-bp ORF was encoded entirely in the second exon together with a 834-bp 3{prime}-untranslated region. The immediate GC-rich 5{prime}-flanking region upstream of exon 1 could serve as a constitutively active promoter in chloramphenicolacetyl-transferase-expression assays. Expression analysis of additional upstream regions suggested the presence of silencer elements between positions -841 and -280. In conclusion, cloning a full-length cDNA permitted cloning of the human IL-8RA gene, identification of the genomic structure, and characterization of the promoter region. 45 refs., 6 figs.

  13. Observation of broad p-wave Feshbach resonances in ultracold $^{85}$Rb-$^{87}$Rb mixtures

    Dong, Shen; Shen, Chuyang; Wu, Yewei; Tey, Meng Khoon; You, Li; Gao, Bo


    We observe new Feshbach resonances in ultracold mixtures of $^{85}$Rb and $^{87}$Rb atoms in the $^{85}$Rb$|2, +2\\rangle$+$^{87}$Rb$|1, +1\\rangle$ and $^{85}$Rb$|2, -2\\rangle$+$^{87}$Rb$|1, -1\\rangle$ scattering channels. The positions and properties of the resonances are predicted and characterized using the semi-analytic multichannel quantum-defect theory by Gao. Of particular interest, a number of broad entrance-channel dominated p-wave resonances are identified, implicating exciting opportunities for studying a variety of p-wave interaction dominated physics.

  14. Tissue microarray immunohistochemical profiles of p53 and pRB in hepatocellular carcinoma and hepatoblastoma.

    Azlin, Abdul Hadi; Looi, Lai Meng; Cheah, Phaik Leng


    The tumour suppressor genes, p53 and pRb, are known to play important roles in neoplastic transformation. While molecular routes to the uncontrolled growth of hepatocytes, leading to primary liver cancer have generated considerable interest, the roles of p53 and pRb mutations in hepatocellular carcinoma (HCC) and hepatoblastoma (HB) remain to be clarified. We examined the immunohistochemical expression of p53 and pRb gene products in 26 HCC and 9 HB, sampled into tissue microarray blocks. 10 (38%) of 26 HCC showed > 10% tumour nuclear staining for p53 protein, 3 of these also being HbsAg positive. Conversely, none of 9 HB expressed nuclear p53 immunopositivity. Some 24 (92%) HCC and 8 (89%) HB showed loss of pRb nuclear expression. Two of the 26 HCC and one of the 9 HB showed >10% tumour nuclear staining for pRb protein. Our results suggest that p53 does not have an important role in the development of HB but may contribute in HCC. There is also loss of pRb expression in the majority of HCC and HB, supporting loss of pRb gene function in the hepatocarcinogenesis pathway. However, a comparison of the staining profiles of p53 and pRb proteins in HCC and HB did not reveal a consistent pattern to differentiate between the two types of tumours immunohistochemically. Hence the use of p53 and pRB protein expression has no contribution in the situation where there is a diagnostic difficulty in deciding between HCC and HB.

  15. New sulfido antimonates of the heavy alkali metals. Synthesis, crystal structure and chemical bonding of (K/Rb/Cs){sub 3}SbS{sub 3} and Cs{sub 3}SbS{sub 4} . H{sub 2}O; Neue Sulfido-Antimonate der schweren Alkalimetalle. Synthese, Kristallstruktur und chemische Bindung von (K/Rb/Cs){sub 3}SbS{sub 3} und Cs{sub 3}SbS{sub 4} . H{sub 2}O

    Schindler, Lisa V.; Schwarz, Michael; Roehr, Caroline [Freiburg Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie


    The new sulfido antimonates(III) (Rb/Cs){sub 3}SbS{sub 3} were prepared from the alkali metal sulfides Rb{sub 2}S/Cs{sub 2}S{sub 2} and elemental antimony and sulfur or Sb{sub 2}S{sub 3} at reaction temperatures of about 700 C. The known isotypic potassium compound was similarly synthesized from the elements. The structures of the light-yellow crystals were refined using single-crystal X-ray data. Both compounds are isotypic to the respective Na salt forming the Na{sub 3}AsS{sub 3} structure type (cubic, space group P2{sub 1}3, K/Rb/Cs: a = 947.21(7)/982.28(5)/1025.92(5) pm, Z = 4, R1 = 0.0159/0.0560/0.0582). The {psi}-tetrahedral SbS{sub 3}{sup 3-} anions with Sb-S bond lengths of 242 pm are arranged in a cubic face centered packing, in which the three crystallographically different A{sup +} cations occupy the tetrahedral and octahedral voids, overall exhibiting a distorted octahedral sulfur coordination. The chemical bonding and the characteristics of the stereochemically active lone electron pair have been investigated by means of FP-LAPW band structure calculations. Needle-shaped crystals of the monohydrate of the antimony(V) salt Cs{sub 3}SbS{sub 4} . H{sub 2}O were obtained from a suspension of Sb{sub 2}O{sub 3}, CsOH and elemental sulfur. Cs{sub 3}SbS{sub 4} . H{sub 2}O crystallizes in a new structure type (monoclinic, space group P2{sub 1}/c, a = 987.17(10), b = 994.83(7), c = 1600.46(14) pm, {beta} = 126.895(8) , Z = 4, R1 = 0.0234). As expected, the Sb-S distances (233.1-234.7 pm) in the nearly ideally tetrahedral anion SbS{sub 4}{sup 3-} are considerably shorter than in the antimonates(III) but match the bond lengths in the anhydrous sulfido antimonate(V) Cs{sub 3}SbS{sub 4}. Due to their similar fcc-like anion packing and the stereochemically active lone electron pair of Sb in the antimonates(III), the whole series of compounds A{sub 3}Sb{sup III,V}S{sub 3/4} shows a uniform structure relation, which is elucidated using crystallographic group

  16. Transcriptional activation by pRB and its coordination with SWI/SNF recruitment.

    Flowers, Stephen; Beck, George R; Moran, Elizabeth


    A central question in cancer biology is why most tumor susceptibility genes are linked with only limited types of cancer. Human germ-line mutation of the retinoblastoma susceptibility gene Rb1 is closely linked with just retinoblastoma and osteosarcoma, although the gene is universally expressed. Functional analysis of pRB and its close relatives, p107 and p130, has largely focused on their roles in repression of proliferation across all tissue types, but genetic evidence indicates an active requirement for pRB in osteoblast differentiation that correlates more directly with osteosarcoma susceptibility. Still, potential promoter targets of pRB and its role in normally differentiating osteoblasts remain insufficiently characterized. Here, an early marker of osteoblast differentiation, alkaline phosphatase, is identified as a direct promoter activation target of pRB. One role of pRB on this promoter is to displace the histone lysine demethylase KDM5A, thereby favoring trimethylation of H3K4, a promoter activation mark. A major new aspect of pRB-mediated transcriptional activation revealed in this promoter analysis is its role in recruitment of an activating SWI/SNF chromatin-remodeling complex. SWI/SNF is a critical coordinator of tissue-specific gene expression. In osteoblasts, SWI/SNF complexes containing the BRM ATPase repress osteoblast-specific genes to maintain the precursor state, whereas the alternative ATPase BRG1 distinguishes an activating SWI/SNF complex necessary for RNA polymerase-II recruitment. A switch from BRM to BRG1 on the alkaline phosphatase promoter marks the onset of differentiation and is accomplished in a precise two-step mechanism. Dissociation of BRM-containing SWI/SNF depends on p300, and association of BRG1-containing SWI/SNF depends on pRB.

  17. A functional connection between pRB and transforming growth factor beta in growth inhibition and mammary gland development.

    Francis, Sarah M; Bergsied, Jacqueline; Isaac, Christian E; Coschi, Courtney H; Martens, Alison L; Hojilla, Carlo V; Chakrabarti, Subrata; Dimattia, Gabriel E; Khoka, Rama; Wang, Jean Y J; Dick, Frederick A


    Transforming growth factor beta (TGF-beta) is a crucial mediator of breast development, and loss of TGF-beta-induced growth arrest is a hallmark of breast cancer. TGF-beta has been shown to inhibit cyclin-dependent kinase (CDK) activity, which leads to the accumulation of hypophosphorylated pRB. However, unlike other components of TGF-beta cytostatic signaling, pRB is thought to be dispensable for mammary development. Using gene-targeted mice carrying subtle missense changes in pRB (Rb1(DeltaL) and Rb1(NF)), we have discovered that pRB plays a critical role in mammary gland development. In particular, Rb1 mutant female mice have hyperplastic mammary epithelium and defects in nursing due to insensitivity to TGF-beta growth inhibition. In contrast with previous studies that highlighted the inhibition of cyclin/CDK activity by TGF-beta signaling, our experiments revealed that active transcriptional repression of E2F target genes by pRB downstream of CDKs is also a key component of TGF-beta cytostatic signaling. Taken together, our work demonstrates a unique functional connection between pRB and TGF-beta in growth control and mammary gland development.

  18. The role of p53 and pRB in apoptosis and cancer

    Hickman, Emma S; Moroni, M Cristina; Helin, Kristian


    Loss of function of both the p53 pathway and the retinoblastoma protein (pRB) pathway plays a significant role in the development of most human cancers. Loss of pRB results in deregulated cell proliferation and apoptosis, whereas loss of p53 desensitizes cells to checkpoint signals, including...... apoptosis. In the past two years, mouse genetics and gene expression profiling have led to major advances in our understanding of how the pRB and p53 pathways regulate apoptosis and thus the development of tumours....

  19. New molybdenum(VI) phosphates: synthesis, characterization, and calculations of centrosymmetric RbMoO2PO4 and noncentrosymmetric Rb4Mo5P2O22.

    Wang, Ying; Pan, Shilie; Su, Xin; Yang, Zhihua; Dong, Lingyun; Zhang, Min


    Two new molybdenum(VI) phosphates, RbMoO(2)PO(4) and Rb(4)Mo(5)P(2)O(22), have been synthesized by standard solid-state reactions, and their structures were determined by single-crystal X-ray diffraction. The former is centrosymmetric, whereas the latter is noncentrosymmetric and chiral. Their crystal structures both consist of corner- and edge-shared MoO(6) octahedra, PO(4) tetrahedra, and RbO(n) (n = 8 or 10) polyhedra and exhibit three- and one-dimensional structures, respectively. Powder second-harmonic generation (SHG) measurements revealed an SHG efficiency of approximately 1.4 × KH(2)PO(4) (KDP) for Rb(4)Mo(5)P(2)O(22). Thermal analysis, infrared and UV-vis-NIR diffuse reflectance spectroscopy, and electronic band structure calculations were also performed on the reported materials. Crystal data are the following: RbMoO(2)PO(4), orthorhombic, space group Fddd (No. 70), a = 11.012(5) Å, b = 12.403(5) Å, c = 15.839(7) Å, V = 2163.3(16) Å(3), and Z = 16; Rb(4)Mo(5)P(2)O(22), orthorhombic, space group C222(1) (No. 20), a = 6.5300(5) Å, b = 19.7834(18) Å, c = 17.3451(15) Å, V = 2240.7(3) Å(3), and Z = 4.

  20. Fractal structure and critical scattering in the three-dimensional percolating antiferromagnet, RbMn{sub 0.31}Mg{sub 0.69}F{sub 3}

    Itoh, S. [Neutron Science Laboratory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801 (Japan)]. E-mail:; Kajimoto, R. [Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai 319-1195 (Japan); Iwasa, K. [Department of Physics, Tohoku University, Sendai 980-8578 (Japan); Aso, N. [Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, Tokai 319-1106 (Japan); Bull, M.J. [ISIS Facility, Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX (United Kingdom); Adams, M.A. [ISIS Facility, Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX (United Kingdom); Takeuchi, T. [Low Temperature Center, Osaka University, Toyonaka 560-0043 (Japan); Yoshizawa, H. [Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, Tokai 319-1106 (Japan)


    We have performed neutron scattering experiments to investigate the static magnetic structure and the magnetic critical scattering in the three-dimensional percolating Heisenberg antiferromagnet, RbMn{sub 0.31}Mg{sub 0.69}F{sub 3}, whose magnetic concentration is just at the percolation concentration for a cubic lattice, c{sub P}=0.312. Magnetic scattering was observed around the superlattice point, (12,12,12). We determined the Neel temperature of this system to be T{sub N}=4.0+/-0.5K, and found that the critical scattering above T{sub N} is similar to that observed in the homogeneous system. At T=1.6K well below T{sub N}, the scattering function is described by a sum of the critical scattering and elastic scattering components, and we demonstrated that the q-variation of the intensity of the elastic scattering component can be described using the fractal dimension.

  1. Synthesis, structural and optical properties of Eu3+-doped ALnP2O7 (A = Cs, Rb, Tl; Ln = Y, Lu, Tm) pyrophosphates phosphors for solid-state lighting

    Mbarek, Aïcha


    A series of 2%Eu3+-activated ALnP2O7 (A = Rb, Cs, Tl; Ln = Y, Lu, Tm) pyrophosphates were synthesized via solid-state reaction method and characterized by X-ray diffraction (XRD), NMR and IR/Raman spectroscopy. Their photoluminescence properties were investigated at room temperature. The phosphors present red emitting luminescence under blue light excitation, based on f-f transitions of Eu3+ ions. Emission spectra showed that the samples had intense and prevailing red emissions at 610 nm belonging to the 5D0→7F2 electric dipole transition. One Eu3+ center was assigned according to the crystal structure and the luminescence characteristics. The decay times were measured monitoring the maximum of emission at λem = 610 nm and exciting in the 5D2 band (λexc = 464 nm). All decay curves were single exponential and lifetimes remain constant with value in integral range 3-4 ms, according to the alkali metal ion. The optical properties show that these host materials are suitable for phosphor materials for solid-state lighting applications.

  2. First-principles calculations of two cubic fluoropervskite compounds: RbFeF3 and RbNiF3

    Mubarak, A. A.; Al-Omari, Saleh


    We present first-principles calculations of the structural, elastic, electronic, magnetic and optical properties for RbFeF3 and RbNiF3. The full-potential linear augmented plan wave (FP-LAPW) method within the density functional theory was utilized to perform the present calculations. We employed the generalized gradient approximation as exchange-correlation potential. It was found that the calculated analytical lattice parameters agree with previous studies. The analysis of elastic constants showed that the present compounds are elastically stable and anisotropic. Moreover, both compounds are classified as a ductile compound. The calculations of the band structure and density functional theory revealed that the RbFeF3 compound has a half-metallic behavior while the RbNiF3 compound has a semiconductor behavior with indirect (M-Γ) band gap. The ferromagnetic behavior was studied for both compounds. The optical properties were calculated for the radiation of up to 40 eV. A beneficial optics technology is predicted as revealed from the optical spectra.

  3. p63 gene structure in the phylum mollusca.

    Baričević, Ana; Štifanić, Mauro; Hamer, Bojan; Batel, Renato


    Roles of p53 family ancestor (p63) in the organisms' response to stressful environmental conditions (mainly pollution) have been studied among molluscs, especially in the genus Mytilus, within the last 15 years. Nevertheless, information about gene structure of this regulatory gene in molluscs is scarce. Here we report the first complete genomic structure of the p53 family orthologue in the mollusc Mediterranean mussel Mytilus galloprovincialis and confirm its similarity to vertebrate p63 gene. Our searches within the available molluscan genomes (Aplysia californica, Lottia gigantea, Crassostrea gigas and Biomphalaria glabrata), found only one p53 family member present in a single copy per haploid genome. Comparative analysis of those orthologues, additionally confirmed the conserved p63 gene structure. Conserved p63 gene structure can be a helpful tool to complement or/and revise gene annotations of any future p63 genomic sequence records in molluscs, but also in other animal phyla. Knowledge of the correct gene structure will enable better prediction of possible protein isoforms and their functions. Our analyses also pointed out possible mis-annotations of the p63 gene in sequenced molluscan genomes and stressed the value of manual inspection (based on alignments of cDNA and protein onto the genome sequence) for a reliable and complete gene annotation.

  4. Non-centrosymmetric Rb2Mn2(MoO43

    Chahira Bouzidi


    Full Text Available The title compound, dirubidium dimanganese(II tris(tetraoxomolybdate, Rb2Mn2(MoO43, was prepared by solid-state reactions. The structure can be described as being composed of MnO6 octahedra sharing corners with MoO4 tetrahedra. The three-dimensional framework contains cavities in which the rubidium ions are located. The Rb+ cations are within distorted nine- and 12-vertex polyhedra. The pairs of different Mn2+ and Rb+ cations are each located on threefold rotation axes.. Rb2Mn2(MoO43 is isotypic with compounds of the Cs2M2Mo3O12 (M = Ni, Fe family. A comparative structural description is provided between the structure of the title compound and those of related phases. Differences with structures such as alluaudite are discussed.

  5. Structures of Hydrated Alkali Metal Cations, M+(H2O)nAr (m = Li, Na, K, rb and Cs, n = 3-5), Using Infrared Photodissociation Spectroscopy and Thermodynamic Analysis

    Ke, Haochen; van der Linde, Christian; Lisy, James M.


    Alkali metal cations play vital roles in chemical and biochemical systems. Lithium is widely used in psychiatric treatment of manic states and bipolar disorder; Sodium and potassium are essential elements, having major biological roles as electrolytes, balancing osmotic pressure on body cells and assisting the electroneurographic signal transmission; Rubidium has seen increasing usage as a supplementation for manic depression and depression treatment; Cesium doped compounds are used as essential catalysts in chemical production and organic synthesis. Since hydrated alkali metal cations are ubiquitous and the basic form of the alkali metal cations in chemical and biochemical systems, their structural and thermodynamic properties serve as the foundation for modeling more complex chemical and biochemical processes, such as ion transport and ion size-selectivity of ionophores and protein channels. By combining mass spectrometry and infrared photodissociation spectroscopy, we have characterized the structures and thermodynamic properties of the hydrated alkali metal cations, i.e. M+(H2O)nAr, (M = Li, Na, K, Rb and Cs, n = 3-5). Ab initio calculations and RRKM-EE (evaporative ensemble) calculations were used to assist in the spectral assignments and thermodynamic analysis. Results showed that the structures of hydrated alkali metal cations were determined predominantly by the competition between non-covalent interactions, i.e. the water---water hydrogen bonding interactions and the water---cation electrostatic interactions. This balance, however, is very delicate and small changes, i.e. different cations, different levels of hydration and different effective temperatures clearly impact the balance.

  6. The structure and expression of the human neuroligin-3 gene.

    Philibert, R A; Winfield, S L; Sandhu, H K; Martin, B M; Ginns, E I


    The neuroligins are a family of proteins that are thought to mediate cell to cell interactions between neurons. During the sequencing at an Xq13 locus associated with a mental retardation syndrome in some studies, we discovered a portion of the human orthologue of the rat neuroligin-3 gene. We now report the structure and the expression of that gene. The gene spans approximately 30kb and contains eight exons. Unlike the rat gene, it codes for at least two mRNAs and at least one of which is expressed outside the CNS. Interestingly, the putative promoter for the gene overlaps the last exon of the neighboring HOPA gene and is located less than 1kb from an OPA element in which a polymorphism associated with mental retardation is found. These findings suggest a possible role for the neuroligin gene in mental retardation and that the role of the gene in humans may differ from its role in rats.

  7. The Rb problem in massive AGB stars.

    Pérez-Mesa, V.; García-Hernández, D. A.; Zamora, O.; Plez, B.; Manchado, A.; Karakas, A. I.; Lugaro, M.


    The asymptotic giant branch (AGB) is formed by low- and intermediate-mass stars (0.8 M_{⊙} develop thermal pulses (TP) and suffer extreme mass loss. AGB stars are the main contributor to the enrichment of the interstellar medium (ISM) and thus to the chemical evolution of galaxies. In particular, the more massive AGB stars (M > 4 M_{⊙}) are expected to produce light (e.g., Li, N) and heavy neutron-rich s-process elements (such as Rb, Zr, Ba, Y, etc.), which are not formed in lower mass AGB stars and Supernova explosions. Classical chemical analyses using hydrostatic atmospheres revealed strong Rb overabundances and high [Rb/Zr] ratios in massive AGB stars of our Galaxy and the Magellanic Clouds (MC), confirming for the first time that the ^{22}Ne neutron source dominates the production of s-process elements in these stars. The extremely high Rb abundances and [Rb/Zr] ratios observed in the most massive stars (specially in the low-metallicity MC stars) uncovered a Rb problem; such extreme Rb and [Rb/Zr] values are not predicted by the s-process AGB models, suggesting fundamental problems in our present understanding of their atmospheres. We present more realistic dynamical model atmospheres that consider a gaseous circumstellar envelope with a radial wind and we re-derive the Rb (and Zr) abundances in massive Galactic AGB stars. The new Rb abundances and [Rb/Zr] ratios derived with these dynamical models significantly resolve the problem of the mismatch between the observations and the theoretical predictions of the more massive AGB stars.

  8. pRb phosphorylation regulates the proliferation of supporting cells in gentamicin-damaged neonatal avian utricle.

    Wu, Jingfang; Sun, Shan; Li, Wenyan; Chen, Yan; Li, Huawei


    The ability of nonmammalian vertebrates to regenerate hair cells (HCs) after damage-induced HC loss has stimulated and inspired research in the field of HC regeneration. The protein pRb encoded by retinoblastoma gene Rb1 forces sensory progenitor cells to exit cell cycle and maintain differentiated HCs and supporting cells (SCs) in a quiescent state. pRb function is regulated by phosphorylation through the MEK/ERK or the pRb/Raf-1 signaling pathway. In our previous study, we have shown that pRb phosphorylation is crucial for progenitor cell proliferation and survival during the early embryonic stage of avian otocyst sensory epithelium development. However, in damaged avian utricle, the role of pRb in regulating the cell cycling of SCs or HCs regeneration still remains unclear. To further elucidate the function of pRb phosphorylation on SCs re-entering the cell cycle triggered by gentamycin-induced HCs damage, we isolated neonatal chicken utricles and treated them with the MEK inhibitor U0126 or the pRb/Raf-1 inhibitor RRD-251, respectively in vitro. We found that after gentamycin-induced HCs damage, pRb phosphorylation is important for the quiescent SCs re-entering the cell cycle in the neonatal chicken utricle. In addition, the proliferation of SCs decreased in a dose-dependent manner in response to both U0126 and RRD-251, which indicates that both the MEK/ERK and the pRb/Raf-1 signaling pathway play important roles in pRb phosphorylation in damaged neonatal chicken utricle. Together, these findings on the function of pRb in damaged neonatal chicken utricle improve our understanding of the regulation of the cell cycle of SCs after HCs loss and may shed light on the mammalian HC regeneration from SCs in damaged organs.

  9. 脑胶质瘤中pRb表达与CDK4、MTS基因异常的相关性研究%Molecular pathological study on expression of pRb and CDK4,MTS gene changes in human gliomas

    田新华; 江澄川; 高翔; 陈商群; 许凯黎; 周瑾


    Objective To investigate expression of pRb and CDK4, MTS gene changes in human gliomas and relationship with the clinical pathology. Methods Brain gliomas with different pathologic types were detected by using PCR-SSCP, Southern blot, Slot blot and immunohistochemistry. Results The negative expression of p16 or pRb and CDK4 amplification often occurred independently. The total rate of negative expression of p16 and/or pRb and/or deletion of p15 and/or CDK4 amplification were in 89% (42/47).Conclusions The propensity was occurrence of singular (89%) rather than combined aberrant expression of p16 or pRb or CDK4 amplification. The suppression of p16, p15 or pRb or the increased activity of CDK4 were sufficient to disrupt this regulatory mechanism in a manner that favors cell proliferation and tissues canceration.%目的 探讨脑胶质瘤中CDK4、MTS基因异常及pRb表达改变与脑胶质瘤发生发展的相关性。方法 应用PCR-SSCP、分子杂交及免疫组化技术检测68例不同病理分级脑胶质瘤。结果 p16基因表达阴性或pRb无表达或CDK4扩增多为单独发生,其中III-IV级肿瘤中pRb、p16蛋白失表达或p15基因缺失或CDK4基因扩增的综合发生率为89%(42/47)。结论 脑胶质瘤中细胞生长周期“关卡”蛋白p16、pRb、或CDK4单因素的异常比交错并发的改变更为常见,p16、pRb失活或CDK4扩增的任一改变,即可能破坏细胞增殖的正常调控,促发脑胶质瘤细胞的癌性增殖或恶性演变。

  10. The extreme COOH terminus of the retinoblastoma tumor suppressor protein pRb is required for phosphorylation on Thr-373 and activation of E2F.

    Gorges, Laura L; Lents, Nathan H; Baldassare, Joseph J


    The retinoblastoma protein pRb plays a pivotal role in G(1)- to S-phase cell cycle progression and is among the most frequently mutated gene products in human cancer. Although much focus has been placed on understanding how the A/B pocket and COOH-terminal domain of pRb cooperate to relieve transcriptional repression of E2F-responsive genes, comparatively little emphasis has been placed on the function of the NH(2)-terminal region of pRb and the interaction of the multiple domains of pRb in the full-length context. Using "reverse mutational analysis" of Rb(DeltaCDK) (a dominantly active repressive allele of Rb), we have previously shown that restoration of Thr-373 is sufficient to render Rb(DeltaCDK) sensitive to inactivation via cyclin-CDK phosphorylation. This suggests that the NH(2)-terminal region plays a more critical role in pRb regulation than previously thought. In the present study, we have expanded this analysis to include additional residues in the NH(2)-terminal region of pRb and further establish that the mechanism of pRb inactivation by Thr-373 phosphorylation is through the dissociation of E2F. Most surprisingly, we further have found that removal of the COOH-terminal domain of either RbDeltaCDK(+T373) or wild-type pRb yields a functional allele that cannot be inactivated by phosphorylation and is repressive of E2F activation and S-phase entry. Our data demonstrate a novel function for the NH(2)-terminal domain of pRb and the necessity for cooperation of multiple domains for proper pRb regulation.

  11. Cardiac (82)Rb PET/CT for fast and non-invasive assessment of microvascular function and structure in asymptomatic patients with type 2 diabetes

    von Scholten, Bernt J; Hasbak, Philip; Christensen, Thomas E


    AIMS/HYPOTHESIS: Coronary flow reserve (CFR) and coronary artery calcium (CAC) represent functional and structural aspects of atherosclerosis. We examined the prevalence of reduced CFR and high CAC scores in three predefined groups of participants without known cardiovascular disease: (1) patients.......026). In multivariate regression analysis, a higher urinary albumin excretion rate (UAER) tended to predict reduced CFR in the total population (p = 0.045). When the CAC score was added, there was also a trend (p = 0.032) towards an inverse association with reduced CFR. CONCLUSIONS/INTERPRETATION: Type 2 diabetic...

  12. Whole chromosome instability resulting from the synergistic effects of pRB and p53 inactivation.

    Manning, A L; Benes, C; Dyson, N J


    Whole chromosome instability (CIN) is a common feature of cancer cells and has been linked to increased tumor evolution and metastasis. Several studies have shown that the loss of the pRB tumor suppressor causes mitotic defects and chromosome mis-segregation. pRB is inactivated in many types of cancer and this raises the possibility that the loss of pRB may be a general cause of CIN in tumors. Paradoxically, retinoblastoma tumor cells have a relatively stable karyotype and currently the circumstances in which pRB inactivation causes CIN in human cancers are unclear. Here we utilize a fluorescence in situ hybridization-based approach to score numerical heterogeneity in chromosome copy number as a readout of CIN. Using this technique, we show that high levels of CIN correlate with the combined inactivation of pRB and p53 and that this association is evident in two independent panels of cancer cell lines. Retinoblastoma cell lines characteristically retain a wild-type TP53 gene, providing an opportunity to test the relevance of this functional relationship. We show that retinoblastoma cell lines display mitotic defects similar to those seen when pRB is depleted from non-transformed cells, but that the presence of wild-type p53 suppresses the accumulation of aneuploid cells. A similar synergy between pRB and p53 inactivation was observed in HCT116 cells. These results suggest that the loss of pRB promotes segregation errors, whereas loss of p53 allows tolerance and continued proliferation of the resulting, genomically unstable cancer cells. Hence, it is the cooperative effect of inactivation of both pRB and p53 tumor suppressor pathways that promotes CIN.

  13. Comparative genomics of the relationship between gene structure and expression

    Ren, X.


    The relationship between the structure of genes and their expression is a relatively new aspect of genome organization and regulation. With more genome sequences and expression data becoming available, bioinformatics approaches can help the further elucidation of the relationships between gene struc

  14. Structure and in vitro transcription of human globin genes.

    Proudfoot, N J; Shander, M H; Manley, J L; Gefter, M L; Maniatis, T


    The alpha-like and beta-like subunits of human hemoglobin are encoded by a small family of genes that are differentially expressed during development. Through the use of molecular cloning procedures, each member of this gene family has been isolated and extensively characterized. Although the alpha-like and beta-like globin genes are located on different chromosomes, both sets of genes are arranged in closely linked clusters. In both clusters, each of the genes is transcribed from the same DNA strand, and the genes are arranged in the order of their expressions during development. Structural comparisons of immediately adjacent genes within each cluster have provided evidence for the occurrence of gene duplication and correction during evolution and have led to the discovery of pseudogenes, genes that have acquired numerous mutations that prevent their normal expression. Recently, in vivo and in vitro systems for studying the expression of cloned eukaryotic genes have been developed as a means of identifying DNA sequences that are necessary for normal gene function. This article describes the application of an in vitro transcription procedure to the study of human globin gene expression.

  15. Assessment of inverse correlation of p16 and pRb expression in carcinoma ex pleomorphic adenoma.

    Tarakji, B; Alenzi, F; Al-Khuraif, A A


    Published data indicate that an inverse correlation has been identified in some tumours such as ovarian cancer and laryngeal squamous carcinoma. This study aimed to characterize alteration in the immunohistochemical expression of p16 and p Rb in carcinoma ex pleomorphic adenoma, and to assess the inverse correlation between p16 and pRb in carcinoma ex pleomorphic adenoma. A selected series of 27 cases of carcinoma ex pleomorphic adenoma were examined at Alfarabi Dental School in 2012. The results showed an inverse correlation between p16 (normal expression) and pRb (mutated) in 15 cases. Also 3 cases showed an inverse correlation between p16 (mutated) and pRb (normal expression). p16 and pRb (both proteins with normal expression) were identified in 3 cases. p16 and pRb (both proteins inactivated) were identified in 6 cases. This study suggests the alteration of p16 and pRb expression has been detected in carcinoma ex pleomorphic adenomas. They mentioned that if the function of one gene such as p16 or pRb was abrogated the other gene would be overexpressed or unaffected ini 18 out of 27 cases.

  16. Syntheses and Structures of the Quaternary Copper Tellurides K 3Ln4Cu 5Te 10 ( Ln=Sm, Gd, Er), Rb 3Ln4Cu 5Te 10 ( Ln=Nd, Gd), and Cs 3Gd 4Cu 5Te 10

    Huang, Fu Qiang; Ibers, James A.


    Six quaternary alkali-metal rare-earth copper tellurides K3Ln4Cu5Te10 (Ln=Sm, Gd, Er), Rb3Ln4Cu5Te10 (Ln=Nd, Gd), and Cs3Gd4Cu5Te10 have been synthesized at 1123 K with the use of reactive fluxes of alkali-metal halides ACl (A=K, Rb, Cs). All crystallographic data were collected at 153 K. These compounds crystallize in space group Pnnm of the orthorhombic system with two formula units in cells of dimensions (A3Ln4, a, b, c (Å)): K3Sm4, 16.590(2), 17.877(2), 4.3516(5); K3Gd4, 16.552(4), 17.767(4), 4.3294(9); K3Er4, 16.460(4), 17.550(4), 4.2926(9); Rb3Nd4, 17.356(1), 17.820(1), 4.3811(3); Rb3Gd4, 17.201(2), 17.586(2), 4.3429(6); Cs3Gd4, 17.512(1), 17.764(1), 4.3697(3). The corresponding R1 indices for the refined structures are 0.0346, 0.0315, 0.0212, 0.0268, 0.0289, and 0.0411. The three K3Ln4Cu5Te10 structures belong to one structure type and the Rb3Ln4Cu5Te10 (Ln=Nd, Gd) and Cs3Gd4Cu5Te10 structures belong to another one, the difference being the location of one of the three unique Cu atoms. Both structure types are three-dimensional tunnel structures that contain similar Ln/Te fragments built from LnTe6 octahedra and CuTe4 tetrahedra. The CuTe4 tetrahedra form 1∞[CuTe5-3] and 1∞[CuTe3-2] chains. The alkali-metal atoms, which are in the tunnels, are coordinated to seven or eight Te atoms.

  17. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.

    Xiao, Guanghua; Wang, Xinlei; Khodursky, Arkady B


    Recent genomic studies have shown that significant chromosomal spatial correlation exists in gene expression of many organisms. Interestingly, coexpression has been observed among genes separated by a fixed interval in specific regions of a chromosome chain, which is likely caused by three-dimensional (3D) chromosome folding structures. Modeling such spatial correlation explicitly may lead to essential understandings of 3D chromosome structures and their roles in transcriptional regulation. In this paper, we explore chromosomal spatial correlation induced by 3D chromosome structures, and propose a hierarchical Bayesian method based on helical structures to formally model and incorporate the correlation into the analysis of gene expression microarray data. It is the first study to quantify and infer 3D chromosome structures in vivo using expression microarrays. Simulation studies show computing feasibility of the proposed method and that, under the assumption of helical chromosome structures, it can lead to precise estimation of structural parameters and gene expression levels. Real data applications demonstrate an intriguing biological phenomenon that functionally associated genes, which are far apart along the chromosome chain, are brought into physical proximity by chromosomal folding in 3D space to facilitate their coexpression. It leads to important biological insight into relationship between chromosome structure and function.

  18. Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

    Zhen Li; Bi-Qing Li; Min Jiang; Lei Chen; Jian Zhang; Lin Liu; Tao Huang


    One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance...

  19. pRb2/p130 protein expression and RBL2 mutation analysis in Burkitt lymphoma from Uganda

    Wabinga Henry


    Full Text Available Abstract Background The members of the retinoblastoma protein family, pRb, p107 and pRb2 (p130, are central players in controlling the cell cycle. Whereas disturbed function of pRb is commonly seen in human cancers, it is still an open question whether pRb2 is involved in tumorigenic processes. However, altered subcellular localization of pRb2 and mutations in the pRb2-encoding gene RBL2 have been described for some tumours, including Burkitt lymphomas (BL. Methods We retrieved 51 biopsy specimens of endemic BL cases from Uganda. The expression of pRb2 was determined by immunohistochemistry. Exons 19–22 of the RBL2 gene, the region known to contain a nuclear localization signal, were screened for mutations by PCR amplification and direct DNA sequencing. Results Nearly all of our cases (84.0% were positive for pRb2 protein expression although this protein is a marker for growth arrest and Burkitt lymphoma is characterized by a high proliferation rate. Of the positive cases, 73.8% were scored as expressing the protein at a high level. Subcellular pRb2 localization was predominantly nuclear and no cases with expression restricted to the cytoplasm were observed. We did not detect any RBL2 mutations in the part of the gene that encodes the C-terminal end of the protein. Conclusion The majority of endemic BL cases from Uganda express pRb2, but somatic RBL2 mutations affecting the protein's nuclear localization signal appear to be rare.

  20. Suppression of genome instability in pRB-deficient cells by enhancement of chromosome cohesion.

    Manning, Amity L; Yazinski, Stephanie A; Nicolay, Brandon; Bryll, Alysia; Zou, Lee; Dyson, Nicholas J


    Chromosome instability (CIN), a common feature of solid tumors, promotes tumor evolution and increases drug resistance during therapy. We previously demonstrated that loss of the retinoblastoma protein (pRB) tumor suppressor causes changes in centromere structure and generates CIN. However, the mechanism and significance of this change was unclear. Here, we show that defects in cohesion are key to the pRB loss phenotype. pRB loss alters H4K20 methylation, a prerequisite for efficient establishment of cohesion at centromeres. Changes in cohesin regulation are evident during S phase, where they compromise replication and increase DNA damage. Ultimately, such changes compromise mitotic fidelity following pRB loss. Remarkably, increasing cohesion suppressed all of these phenotypes and dramatically reduced CIN in cancer cells lacking functional pRB. These data explain how loss of pRB undermines genomic integrity. Given the frequent functional inactivation of pRB in cancer, conditions that increase cohesion may provide a general strategy to suppress CIN.

  1. Structure and Function of Cytochrome P-450 Genes


    UNIT Bolling Air Force Base, D.C. 20332 ELEMENT NO. NO. NO. ACCESSION NO. 61102F 2312 A5 11. TITLE (Include Security Clasification ) Structure and...chromatin structure of these genes and to characterize nuclear proteins that bind to the genes. Accesion For hRIS A-RA&I d OVIrC TAB LISUrc’t,:oimnc...nuclear proteins that bind to the genes. ........ .. A. RESEARCH OBJECTIVES The overall goal and the specific aims of this project remain the same as

  2. Increased complexity of gene structure and base composition in vertebrates

    Ying Wu; Huizhong Yuan; Shengjun Tan; Jian-Qun Chen; Dacheng Tian; Haiwang Yang


    How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals: human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3' UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results.We also find that GC-content increased in many gene regions (especially 5' UTR) in the evolution of endotherms, except in coding-exons.Analysis of individual genomes shows that 3′ UTR demonstrated stronger length and CC-content correlation with intron than 5' UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.

  3. Crystal structures of new alkali metal-rich oxometallates. Rubidium aluminate tetrahydroxide, Rb{sub 9}(AlO{sub 4})(OH){sub 4}, rubidium orthogallate, Rb{sub 5}GaO{sub 4}, cesium bis-chromate(IV) oxide, Cs{sub 10}(CrO{sub 4}){sub 2}O, and cesium diindate, Cs{sub 8}In{sub 2}O{sub 7}

    Bender, Johannes; Wohlfarth, Andreas; Hoch, Constantin [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)


    Several new alkali metal oxometallates with anions built up from tetrahedral [MO{sub 4}] units were obtained in reactions aimed at the formation of alkali metal suboxometallates or by thermally decomposing the latter. Rubidium orthoaluminate tetrahydroxide Rb{sub 9}(AlO{sub 4})(OH){sub 4} crystallizes with a new structure type (space group P2{sub 1}/c, a = 13.116(1), b = 6.9266(5), c = 18.934(2) A, {beta} = 92.05(1) , V = 1719.0(3) A{sup 3}, Z = 4, R1 = 0.0352) and contains orthoaluminate anions [AlO{sub 4}]{sup 5-} and isolated hydroxide anions. Rubidium orthogallate Rb{sub 5}GaO{sub 4} crystallizes with the Na{sub 5}GaO{sub 4} structure type (space group Pbca, a = 6.9318(5), b = 21.309(2), c = 11.740(1) A, V = 1734.2(3) A{sup 3}, Z = 8, R1 = 0.0423) with isolated orthogallate anions [GaO{sub 4}]{sup 5-}. Cesium chromate oxide Cs{sub 10}(CrO{sub 4}){sub 2}O adopts the Cs{sub 10}(GeO{sub 4}){sub 2}O structure type (space group P2{sub 1}/c, a = 12.903(1), b = 11.4523(8), c = 19.074(3) A, {beta} = 127.903(8) , V = 2223.9(4) A{sup 3}, Z = 4, R1 = 0.0326) with orthochromate(IV) anions [CrO{sub 4}]{sup 4-} and isolated oxide anions. In all orthometallates the anions [MO{sub 4}]{sup n-} deviate only slightly from ideal tetrahedral symmetry. Cesium diindate Cs{sub 8}In{sub 2}O{sub 7} crystallizes with the Cs{sub 8}Fe{sub 2}O{sub 7} structure type (space group P2{sub 1}/c, a = 7.4307(6), b = 18.6181(14), c = 7.2639(6) A {beta} = 119.225(8) , V = 877.0(1) A{sup 3}, Z = 2, R1 = 0.0349). A single-crystal structure investigation at r.t. has shown linear diindate units, but the temperature dependence of the libration angles from TLS studies for the bridging oxygen atom suggests a slightly bent and dynamically disordered diindate anion. (orig.)

  4. Gene-based and semantic structure of the Gene Ontology as a complex network

    Coronnello, Claudia; Tumminello, Michele; Miccichè, Salvatore


    The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The Gene Ontology (GO) is constantly evolving over time. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. Here we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium. Moreover, the GO is a natural example of bipartite network of terms and genes. Here we are interested in studying the properties of the projected network of terms, i.e. a gene-based weighted network of GO terms, in which a link between any two terms is set if at least one gene is annotated in both terms. One aim of the present paper is to compare the structural properties of the semantic and the gene-based network. The relative importance of terms is very similar in the two networks, but the community structure changes. We show that in some cases GO terms that appear to be distinct from a semantic point of view are instead connected, and appear in the same community when considering their gene content. The identification of such gene-based communities of terms might therefore be the basis of a simple protocol aiming at improving the semantic structure of GO. Information about terms that share large gene content might also be important from a biomedical point of view, as it might reveal how genes over-expressed in a certain term also affect other biological processes, molecular functions and cellular components not directly linked according to GO semantics.

  5. Divergence of the mRNA targets for the Ssb proteins of bacteriophages T4 and RB69

    Petrov Vasiliy M


    Full Text Available Abstract The single-strand binding (Ssb protein of phage T4 (T4 gp32, product of gene 32 is a mRNA-specific autogenous translational repressor, in addition to being a sequence-independent ssDNA-binding protein that participates in phage DNA replication, repair and recombination. It is not clear how this physiologically essential protein distinguishes between specific RNA and nonspecific nucleic acid targets. Here, we present phylogenetic evidence suggesting that ssDNA and specific RNA bind the same gp32 domain and that plasticity of this domain underlies its ability to configure certain RNA structures for specific binding. We have cloned and characterized gene 32 of phage RB69, a relative of T4 We observed that RB69 gp32 and T4 gp32 have nearly identical ssDNA binding domains, but diverge in their C-terminal domains. In T4 gp32, it is known that the C-terminal domain interacts with the ssDNA-binding domain and with other phage-induced proteins. In translation assays, we show that RB69 gp32 is, like T4 gp32, an autogenous translational repressor. We also show that the natural mRNA targets (translational operators for the 2 proteins are diverged in sequence from each other and yet can be repressed by either gp32. Results of chemical and RNase sensitivity assays indicate that the gp32 mRNA targets from the 2 related phages have similar structures, but differ in their patterns of contact with the 2 repressors. These and other observations suggest that a range of gp32-RNA binding specificities may evolve in nature due to plasticity of the protein-nucleic acid interaction and its response to modulation by the C-terminal domain of this translational repressor.

  6. E2F-1 binding affinity for pRb is not the only determinant of the E2F-1 activity.

    Sahin, Fikret; Sladek, Todd L


    E2F-1 is the major cellular target of pRB and is regulated by pRB during cell proliferation. Interaction between pRB and E2F-1 is dependent on the phosphorylation status of pRB. Despite the fact that E2F-1 and pRB have antagonistic activities when they are overexpressed, the role of the E2F-1-pRB interaction in cell growth largely remains unknown. Ideally, it would be better to study the properties of a pRB mutant that fails to bind to E2F, but retains all other activities. To date, no pRB mutation has been characterized in sufficient detail to show that it specifically eliminates E2F binding but leaves other interactions intact. An alternative approach to this issue is to ask whether mutations that change E2F proteins binding affinity to pRB are sufficient to change cell growth in aspect of cell cycle and tumor formation. Therefore, we used the E2F-1 mutants including E2F-1/S332-7A, E2F-1/S375A, E2F-1/S403A, E2F-1/Y411A and E2F-1/L132Q that have different binding affinities for pRB to better understand the roles of the E2F-1 phosphorylation and E2F-1-pRB interaction in the cell cycle, as well as in transformation and gene expression. Data presented in this study suggests that in vivo phosphorylation at amino acids 332-337, 375 and 403 is important for the E2F-1 and pRB interaction in vivo. However, although E2F-1 mutants 332-7, 375 and 403 showed similar binding affinity to pRB, they showed different characteristics in transformation efficiency, G(0) accumulation, and target gene experiments.

  7. The sub-cellular localisation of the potato (Solanum tuberosum L.) carotenoid biosynthetic enzymes, CrtRb2 and PSY2.

    Pasare, Stefania; Wright, Kathryn; Campbell, Raymond; Morris, Wayne; Ducreux, Laurence; Chapman, Sean; Bramley, Peter; Fraser, Paul; Roberts, Alison; Taylor, Mark


    Carotenoids are isoprenoids with important biological roles both for plants and animals. The yellow flesh colour of potato (Solanum tuberosum L.) tubers is a quality trait dependent on the types and levels of carotenoids that accumulate. The carotenoid biosynthetic pathway is well characterised, facilitating the successful engineering of carotenoid content in numerous crops including potato. However, a clear understanding concerning the factors regulating carotenoid accumulation and localisation in plant storage organs, such as tubers, is lacking. In the present study, the localisation of key carotenoid biosynthetic enzymes was investigated, as one of the unexplored factors that could influence the accumulation of carotenoids in potato tubers. Stable transgenic potato plants were generated by over-expressing β-CAROTENE HYDROXYLASE 2 (CrtRb2) and PHYTOENE SYNTHASE 2 (PSY2) genes, fused to red fluorescent protein (RFP). Gene expression and carotenoid levels were both significantly increased, confirming functionality of the fluorescently tagged proteins. Confocal microscopy studies revealed different sub-organellar localisations of CrtRb2-RFP and PSY2-RFP within amyloplasts. CrtRb2 was detected in small vesicular structures, inside amyloplasts, whereas PSY2 was localised in the stroma of amyloplasts. We conclude that it is important to consider the location of biosynthetic enzymes when engineering the carotenoid metabolic pathway in storage organs such as tubers.

  8. Susceptibility of pRb-deficient epidermis to chemical skin carcinogenesis is dependent on the p107 allele dosage.

    Santos, Mirentxu; Ruiz, Sergio; Lara, M Fernanda; Segrelles, Carmen; Moral, Marta; Martínez-Cruz, Ana Belén; Ballestín, Claudio; Lorz, Corina; García-Escudero, Ramón; Paramio, Jesús M


    Functional inactivation of the pRb-dependent pathway is a general feature of human cancer. However, only a reduced spectrum of tumors displays inactivation of the Rb gene. This can be attributed, at least partially, to the possible overlapping functions carried out by the related retinoblastoma family members p107 and p130. We observed that loss of pRb in epidermis, using the Cre/LoxP technology, results in proliferation and differentiation defects. These alterations are partially compensated by the elevation in the levels of p107. Moreover, epidermis lacking pRb and p107, but not pRb alone, develops spontaneous tumors, and double deficient primary keratinocytes are highly susceptible to Ha-ras-induced transformation. Two-stage chemical carcinogenesis experiments in mice lacking pRb in epidermis revealed a reduced susceptibility in papilloma formation and an increase in the malignant conversion. We have now explored whether the loss of one p107 allele, inducing a decrease in the levels of p107 up to normal levels could restore the susceptibility of pRb-deficient skin to two-stage protocol. We observed partial restoration in the incidence, number, and size of tumors. However, there is no increased malignancy despite sustained p53 activation. We also observed a partial reduction in the levels of proapoptotic proteins in benign papillomas. These data confirm our previous suggestions on the role of p107 as a tumor suppressor in epidermis in the absence of pRb.

  9. Charge transfer in the cold Yb$^+$ + Rb collisions

    Sayfutyarova, Elvira R; Yakovleva, Svetlana A; Belyaev, Andrey K


    Charge-transfer cold Yb$^+$ + Rb collision dynamics is investigated theoretically using high-level {\\it ab initio} potential energy curves, dipole moment functions and nonadiabatic coupling matrix elements. Within the scalar-relativistic approximation, the radiative transitions from the entrance $A^1\\Sigma^+$ to the ground $X^1\\Sigma^+$ state are found to be the only efficient charge-transfer pathway. The spin-orbit coupling does not open other efficient pathways, but alters the potential energy curves and the transition dipole moment for the $A-X$ pair of states. The radiative, as well as the nonradiative, charge-transfer cross sections calculated within the $10^{-3}-10$ cm$^{-1}$ collision energy range exhibit all features of the Langevin ion-atom collision regime, including a rich structure associated with centrifugal barrier tunneling (orbiting) resonances. Theoretical rate coefficients for two Yb isotopes agree well with those measured by immersing Yb$^+$ ion in an ultracold Rb ensemble in a hybrid trap....

  10. Exploring strategies for the production of ultracold RbYb molecules in conservative traps

    Bruni, Cristian


    Within the scope of this thesis, the production of ultracold molecules at a temperature of a few μK with various isotopes of rubidium (Rb) and ytterbium (Yb) was examined by means of photoassociation spectroscopy and magnetic Feshbach resonances in combined conservative traps. The long-term goal of this experiment is the production of ultracold RbYb molecules in the rovibronic ground state. It was possible to produce electronically excited {sup 87}Rb {sup 176}Yb molecules in a novel hybrid trap (HT) at a combined temperature of 1.7 μK by means of 1-photon photoassociation close to the Rb D1 line at 795 nm. This HT takes advantage of the different magnetic properties of Rb and Yb and allows for independent trapping and manipulation of the atomic species. It combines an Ioffe-Pritchard type magnetic trap for Rb and a near-resonant optical dipole trap for Yb. The excited molecular {sup 2}Π{sub 1/2} state could be characterized further extending previous works in a combined MOT and vibrational levels reaching binding energies up to E{sub b}=-h x 2.2 THz could be assigned by trap-loss spectroscopy. Almost every detected vibrational state consists of two resonances that could be assigned to the molecular analogue of the hyperfine structure of {sup 87}Rb. An important experimental observation is a decrease in hyperfine splitting with increasing binding energy of a vibrational level. For the deepest found vibrational state the hyperfine splitting amounts only 70 % of the atomic value (817 MHz) which emphasizes a gradual passage from weakly to tightly bound molecules. Furthermore, detailed attempts were undertaken to induce magnetic Feshbach resonances in {sup 85}Rb and different Yb isotopes, especially {sup 171}Yb in a crossed optical dipole trap at 1064 nm at temperatures of 10 μK. For this purpose, a homogeneous magnetic field was applied and scanned in small steps over the range of 495 G ∼ 640 G. Unfortunately, our efforts were without success. Additionally, well

  11. Structural basis of eukaryotic gene transcription.

    Boeger, Hinrich; Bushnell, David A; Davis, Ralph; Griesenbeck, Joachim; Lorch, Yahli; Strattan, J Seth; Westover, Kenneth D; Kornberg, Roger D


    An RNA polymerase II promoter has been isolated in transcriptionally activated and repressed states. Topological and nuclease digestion analyses have revealed a dynamic equilibrium between nucleosome removal and reassembly upon transcriptional activation, and have further shown that nucleosomes are removed by eviction of histone octamers rather than by sliding. The promoter, once exposed, assembles with RNA polymerase II, general transcription factors, and Mediator in a approximately 3 MDa transcription initiation complex. X-ray crystallography has revealed the structure of RNA polymerase II, in the act of transcription, at atomic resolution. Extension of this analysis has shown how nucleotides undergo selection, polymerization, and eventual release from the transcribing complex. X-ray and electron crystallography have led to a picture of the entire transcription initiation complex, elucidating the mechanisms of promoter recognition, DNA unwinding, abortive initiation, and promoter escape.

  12. RB975952 – Early maturing sugarcane cultivar

    Monalisa Sampaio Carneiro


    Full Text Available RB975952 is an early maturing sugarcane cultivar released for the South-Central region of Brazil. It should be harvested between April and May, and it is recommended for planting in environments with medium to high production potential. RB975952 has high resistance levels to the main diseases of the crop, it also has a good shoot development after mechanical harvesting, and high sucrose yields.

  13. Lysine methylation regulates the pRb tumour suppressor protein.

    Munro, S; Khaire, N; Inche, A; Carr, S; La Thangue, N B


    The pRb tumour suppressor protein has a central role in coordinating early cell cycle progression. An important level of control imposed on pRb occurs through post-translational modification, for example, phosphorylation. We describe here a new level of regulation on pRb, mediated through the targeted methylation of lysine residues, by the methyltransferase Set7/9. Set7/9 methylates the C-terminal region of pRb, both in vitro and in cells, and methylated pRb interacts with heterochromatin protein HP1. pRb methylation is required for pRb-dependent cell cycle arrest and transcriptional repression, as well as pRb-dependent differentiation. Our results indicate that methylation can influence the properties of pRb, and raise the interesting possibility that methylation modulates pRb tumour suppressor activity.


    龙江斌; 区宝祥; 梁启万; 李辉梅


    By southern hybridization with 1.8 kb cDNA probe,a high freqnency (40.5%) of structural abnormality of p 53 gene was observed in primary nasopharyngeal carcinoma (NPC) biopsies. The regioas of exons 1 to 4 of the gene were examined by poiymerase chain reaction-single strand conformation polymorphism, no point nmtation was found. Because very low rate of point mutation had been reported in exons 5 to 8,we considered that structural ahnormality in the region of exons 1 to 8 of the gene might be uncommon in NPC. The speetrophotometer scaaning analysis of outoradiograms and rehybridization investigation of nitrocellulose filter with exon 11 probe indicated that most of structure aberrations we observed might be rearrangement occurring in exon ll.

  15. RB: An essential player in adult neurogenesis.

    Fong, Bensun C; Slack, Ruth S


    The fundamental mechanisms underlying adult neurogenesis remain to be fully clarified. Members of the cell cycle machinery have demonstrated key roles in regulating adult neural stem cell (NSC) quiescence and the size of the adult-born neuronal population. The retinoblastoma protein, Rb, is known to possess CNS-specific requirements that are independent from its classical role as a tumor suppressor. The recent study by Vandenbosch et al. has clarified distinct requirements for Rb during adult neurogenesis, in the restriction of proliferation, as well as long-term adult-born neuronal survival. However, Rb is no longer believed to be the main cell cycle regulator maintaining the quiescence of adult NSCs. Future studies must consider Rb as part of a larger network of regulatory effectors, including the other members of the Rb family, p107 and p130. This will help elucidate the contribution of Rb and other pocket proteins in the context of adult neurogenesis, and define its crucial role in regulating the size and fate of the neurogenic niche.

  16. New alkali metal diphosphates how materials to preserve the security of the environment: CsNaCu(P2O7), Rb2Cu(P2O7) and CsNaCo(P2O7) synthesis and crystal structure determination

    Chernyatieva, Anastasiya; Filatova, Alyona; Spiridonova, Dariya; Krivovichev, Sergey


    In this work we describe preliminary results of the synthesis and of a crystal-chemical study of synthetic phosphates with transition metals. Due to the increasing requirements for environmental safety specialists from various industries, we are searching for sustainable forms of immobilization of hazardous waste during storage. We are also developing a component-based waste for new materials. In our continued exploratory synthesis of compounds containing transition-metals, we were able to produce the new diphosphate phases CsNaCu(P2O7), Rb2Cu(P2O7) and CsNaCo(P2O7). A crystal chemical study has allowed us to identify new phosphates. Crystals of CsNaCu(P2O7) (Phase 1) is orthorhombic, crystallizes in space group Pmn21, with a = 5.147(8), b = 15.126(2), c = 9.717(2) Å, V = 756.20 Å3, R1 = 0.066 and Rb2Cu(P2O7) (Phase 2) is orthorhombic as well, crystallizes in space group Pmcn, with a = 5.183(8), b = 10.096(1), c = 15.146(3) Å, V = 793.55 Å3, R1 = 0.063, they have been obtained by high-temperature reaction of RbNO3, CsNO3, Cu(NO3)2, NaOH and (NH4)4P2O7. Synthetic crystals of the phosphate of copper and rubidium were studied in detail by us on the structures of Rb2Cu(P2O7) and Rb2Cu3(P2O7)2 - new alkali metal copper diphosphates (CHERNYATIEVA et al., 2008). Here we report the synthesis, the structure and the properties of the title compounds and we compare these phases with the previously discovered K2CuP2O7 (ELMAADI et al., 1995) and CsNaMnP2O7 (HUANG et al., 1998). These structures crystallize in other space groups, although their structures are also based on 2-D layers, formed by P2O7 groups combined with polyhedra of the transition metals (CHERNYATIEVA et al., 2012). A crystal chemical study has allowed us to identify even new diphosphates CsNaCu(P2O7) (Phase 3). Crystals of CsNaCoP2O7 is monoclinic, space group P 21/n, with a = 7,424(2), b = 7,648(1), c = 12,931(3)Å, β = 90,71(2)° , V = 734.2(3) Å3 and R1 = 0.060. The structure is based framework of Co

  17. Half metallic ferromagnetism in alkali metal nitrides MN (M = Rb, Cs): A first principles study

    Murugan, A., E-mail:; Rajeswarapalanichamy, R., E-mail:; Santhosh, M., E-mail:; Sudhapriyanga, G., E-mail: [Department of Physics, N.M.S.S.V.N College, Madurai, Tamilnadu-625019 (India); Kanagaprabha, S. [Department of Physics, Kamaraj College, Tuticorin, Tamil Nadu-628003 (India)


    The structural, electronic and elastic properties of two alkali metal nitrides (MN: M= Rb, Cs) are investigated by the first principles calculations based on density functional theory using the Vienna ab-initio simulation package. At ambient pressure the two nitrides are stable in ferromagnetic state with CsCl structure. The calculated lattice parameters are in good agreement with the available results. The electronic structure reveals that these materials are half metallic in nature. A pressure-induced structural phase transition from CsCl to ZB phase is observed in RbN and CsN.

  18. Long Non-Coding RNAs Embedded in the Rb and p53 Pathways

    Subramanian, Murugan; Jones, Matthew F.; Lal, Ashish, E-mail: [Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States)


    In recent years, long non-coding RNAs (lncRNAs) have gained significant attention as a novel class of gene regulators. Although a small number of lncRNAs have been shown to regulate gene expression through diverse mechanisms including transcriptional regulation, mRNA splicing and translation, the physiological function and mechanism of action of the vast majority are not known. Profiling studies in cell lines and tumor samples have suggested a potential role of lncRNAs in cancer. Indeed, distinct lncRNAs have been shown to be embedded in the p53 and Rb networks, two of the major tumor suppressor pathways that control cell cycle progression and survival. Given the fact that inactivation of Rb and p53 is a hallmark of human cancer, in this review we discuss recent evidence on the function of lncRNAs in the Rb and p53 signaling pathways.

  19. p16INK4a, but not constitutively active pRb, can impose a sustained G1 arrest: molecular mechanisms and implications for oncogenesis

    Lukas, J; Sørensen, Claus Storgaard; Lukas, C


    p16ink4 and pRb, two components of a key G1/S regulatory pathway, and tumor suppressors commonly targeted in oncogenesis, are among the candidates for gene therapy of cancer. Wild-type p16 and a constitutively active pRb(delta cdk) mutant both blocked G1 in short-term experiments, but only p16...

  20. Synthesis, single-crystal structure determination and Raman spectra of the tricyanomelaminates NaA{sub 5}[C{sub 6}N{sub 9}]{sub 2} . 4 H{sub 2}O (A = Rb, Cs)

    Reckeweg, Olaf; DiSalvo, Francis J. [Cornell Univ., Ithaca, NY (United States). Baker Lab.; Schulz, Armin [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)


    Transparent colorless crystals of NaA{sub 5}[C{sub 6}N{sub 9}]{sub 2} . 4 H{sub 2}O (A = Rb, Cs) were obtained by blending aqueous solutions of Na{sub 3}[C{sub 6}N{sub 9}] and RbF or CsF, respectively, and subsequent evaporation of the water under ambient conditions. Both compounds crystallize in the space group P2{sub 1}/m (no. 11) with the cell parameters a = 815.56(16), b = 1637.7(4) and c = 1036.4(3) pm, and β = 110.738(12) for NaRb{sub 5}[C{sub 6}N{sub 9}]{sub 2} . 4 H{sub 2}O and a = 843.32(6), b = 1708.47(11) and c = 1052.42(7) pm, and β = 112.034(2) for NaCs{sub 5}[C{sub 6}N{sub 9}]{sub 2} . 4 H{sub 2}O, respectively. Raman spectra of the title compounds complement our results.

  1. Synthesis and structures of type-I clathrates: Rb6Na2Ge44.89(1), Cs6Na2Zn4Ge42 and Cs6.40(1)Na1.60(1)Ga8Ge38

    Zhang, Hui; Mu, Gang; Huang, Fuqiang; Xie, Xiaoming


    Type-I clathrates of Rb6Na2Ge44.89(1), Cs6Na2Zn4Ge42 and Cs6.40(1)Na1.60(1)Ga8Ge38 were synthesized via solid-state reaction. Rb6Na2Ge44.89(1), Cs6Na2Zn4Ge42 and Cs6.40(1)Na1.60(1)Ga8Ge38 were found to crystalize in the cubic space group of Pm 3 ̅ n with lattice parameters of a=10.72755(5) Å, a=10.79501(8) Å and a=10.79726(5) Å, respectively. Theoretical calculations indicated semiconducting features for the calculation models of Rb6Na2Ge44, Cs6Na2Zn4Ge42 and Cs6Na2Ga8Ge38 with band gaps of 0.002 eV, 0.297 eV and 0.221 eV, respectively.

  2. Electronic parameters and top surface chemical stability of RbPb{sub 2}Br{sub 5}

    Atuchin, V.V., E-mail: [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Isaenko, L.I. [Laboratory of Crystal Growth, Institute of Geology and Mineralogy, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Kesler, V.G. [Laboratory of Physical Principles for Integrated Microelectronics, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Pokrovsky, L.D. [Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, SB RAS, Novosibirsk 90, 630090 (Russian Federation); Tarasova, A.Yu. [Laboratory of Crystal Growth, Institute of Geology and Mineralogy, SB RAS, Novosibirsk 90, 630090 (Russian Federation)


    Highlights: Black-Right-Pointing-Pointer Bridgman growth of RbPb{sub 2}Br{sub 5} crystal. Black-Right-Pointing-Pointer Electronic structure measurements with XPS. Black-Right-Pointing-Pointer Optical crystalline surface fabrication. - Abstract: The RbPb{sub 2}Br{sub 5} crystal has been grown by Bridgman method. The electronic structure of RbPb{sub 2}Br{sub 5} has been measured with XPS for a powder sample. High chemical stability of RbPb{sub 2}Br{sub 5} surface is verified by weak intensity of O 1s core level recorded by XPS and structural RHEED measurements. Chemical bonding effects have been observed by the comparative analysis of element core levels and crystal structure of RbPb{sub 2}Br{sub 5} and several rubidium- and lead-containing bromides using binding energy difference parameters {Delta}{sub Rb} = (BE Rb 3d - BE Br 3d) and {Delta}{sub Pb} = (BE Pb 4f{sub 7/2} - BE Br 3d).

  3. Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation

    Kansara, Maya; Leong, Huei San; Lin, Dan Mei; Popkiss, Sophie; Pang, Puiyi; Garsed, Dale W.; Walkley, Carl R.; Cullinane, Carleen; Ellul, Jason; Haynes, Nicole M.; Hicks, Rod; Kuijjer, Marieke L.; Cleton-Jansen, Anne-Marie; Hinds, Philip W.; Smyth, Mark J.; Thomas, David M.


    Ionizing radiation (IR) and germline mutations in the retinoblastoma tumor suppressor gene (RB1) are the strongest risk factors for developing osteosarcoma. Recapitulating the human predisposition, we found that Rb1+/– mice exhibited accelerated development of IR-induced osteosarcoma, with a latency of 39 weeks. Initial exposure of osteoblasts to carcinogenic doses of IR in vitro and in vivo induced RB1-dependent senescence and the expression of a panel of proteins known as senescence-associated secretory phenotype (SASP), dominated by IL-6. RB1 expression closely correlated with that of the SASP cassette in human osteosarcomas, and low expression of both RB1 and the SASP genes was associated with poor prognosis. In vivo, IL-6 was required for IR-induced senescence, which elicited NKT cell infiltration and a host inflammatory response. Mice lacking IL-6 or NKT cells had accelerated development of IR-induced osteosarcomas. These data elucidate an important link between senescence, which is a cell-autonomous tumor suppressor response, and the activation of host-dependent cancer immunosurveillance. Our findings indicate that overcoming the immune response to senescence is a rate-limiting step in the formation of IR-induced osteosarcoma. PMID:24231354

  4. Loss of pRB causes centromere dysfunction and chromosomal instability.

    Manning, Amity L; Longworth, Michelle S; Dyson, Nicholas J


    Chromosome instability (CIN) is a common feature of tumor cells. By monitoring chromosome segregation, we show that depletion of the retinoblastoma protein (pRB) causes rates of missegregation comparable with those seen in CIN tumor cells. The retinoblastoma tumor suppressor is frequently inactivated in human cancers and is best known for its regulation of the G1/S-phase transition. Recent studies have shown that pRB inactivation also slows mitotic progression and promotes aneuploidy, but reasons for these phenotypes are not well understood. Here we describe the underlying mitotic defects of pRB-deficient cells that cause chromosome missegregation. Analysis of mitotic cells reveals that pRB depletion compromises centromeric localization of CAP-D3/condensin II and chromosome cohesion, leading to an increase in intercentromeric distance and deformation of centromeric structure. These defects promote merotelic attachment, resulting in failure of chromosome congression and an increased propensity for lagging chromosomes following mitotic delay. While complete loss of centromere function or chromosome cohesion would have catastrophic consequences, these more moderate defects allow pRB-deficient cells to proliferate but undermine the fidelity of mitosis, leading to whole-chromosome gains and losses. These observations explain an important consequence of RB1 inactivation, and suggest that subtle defects in centromere function are a frequent source of merotely and CIN in cancer.

  5. Contribution to the study of {beta} disintegration and of nuclear structure using experiments on certain {beta}-{gamma} cascades: 198{sub Au}, 86{sub Rb}, 170{sub Tm}; Contribution a l'etude de la desintegration beta et a l'etude de la structure nucleaire a l'aide d'experiences sur certaines cascades beta-gamma: 198{sub Au}, 86{sub Rb}, 170{sub Tm}

    Lachkar, J. [Commissariat a l' Energie Atomique, Bruyeres-le-Chatel (France). Centre d' Etudes; Paris-11 Univ., fabulte des Sciences 91 - Orsay (France)


    {beta}{gamma} directional angular correlations and shapes of inner beta spectra leading to the first excited level of the final nucleus enable one to determine the nuclear matrix elements typical of the {beta} transition. In the three observed first forbidden cases: {sup 170}Tm, {sup 86}Rb, {sup 198}Au, these matrix elements do not confirm the independent shell model theory. Other hypotheses are then suggested and discussed. (author) [French] Les experiences de correlation angulaire {beta}{gamma} et l'etude du spectre {beta} conduisant au premier niveau excite du noyau final permettent de determiner les elements de matrices nucleaires caracteristiques de cette transition. Dans les trois cas etudies (transitions une fois interdites): {sup 170}Tm, {sup 86}Rb, {sup 198}Au, ces elements de matrices ne peuvent etre retrouves a l'aide du modele en couches et a particules independantes. D'autres hypotheses sont alors emises et discutees. (auteur)

  6. Synthesis and tunable luminescence of RbCaGd(PO4)2:Ce3+, Mn2+ phosphors

    Chen, Xue; Lv, Fengzhu; Li, Penggang; Zhang, Yihe


    RbCaGd(PO4)2 doped with Ce3+, Mn2+ was synthesized by the sol-gel method. The crystal structure and crystallographic location of Ce3+ in RbCaGd(PO4)2 were identified by Rietveld refinement. Powder X-ray diffraction (XRD) revealed that the structure of RbCaGd(PO4)2:Ce3+ compounds is hexagonal structure which is similar to that of hexagonal LnPO4 with the lattice constant of a = b = 7.005(57) Å, c = 6.352(05) Å, and V (cell volume) = 269.980 Å3. The photoluminescence behavior and emission mechanism were studied systematically by doping activators in the RbCaGd(PO4)2 host. The Mn2+ incorporated RbCaGd(PO4)2:Ce3+, Mn2+ compounds exhibited blue emission from the parity- and spin-allowed f-d transition of Ce3+ and orange-to-red emission from the forbidden 4T1 → 6A1 transition of Mn2+. The emission chromaticity coordinates of RbCaGd(PO4)2:0.10Ce3+, xMn2+ (x = 0.16, 0.25) are close to the white region due to an energy transfer process and the energy transfer mechanism from Ce3+ to Mn2+ in the RbCaGd(PO4)2 host was dominated by dipole-dipole interactions.

  7. Variation within the Huntington's disease gene influences normal brain structure.

    Mark Mühlau

    Full Text Available Genetics of the variability of normal and diseased brain structure largely remains to be elucidated. Expansions of certain trinucleotide repeats cause neurodegenerative disorders of which Huntington's disease constitutes the most common example. Here, we test the hypothesis that variation within the IT15 gene on chromosome 4, whose expansion causes Huntington's disease, influences normal human brain structure. In 278 normal subjects, we determined CAG repeat length within the IT15 gene on chromosome 4 and analyzed high-resolution T1-weighted magnetic resonance images by the use of voxel-based morphometry. We found an increase of GM with increasing long CAG repeat and its interaction with age within the pallidum, which is involved in Huntington's disease. Our study demonstrates that a certain trinucleotide repeat influences normal brain structure in humans. This result may have important implications for the understanding of both the healthy and diseased brain.

  8. Single crystals of LnFeAsO{sub 1-x}F{sub x} (Ln = La, Pr, Nd, Sm, Gd) and Ba{sub 1-x}Rb{sub x}Fe{sub 2}As{sub 2}: Growth, structure and superconducting properties

    Karpinski, J., E-mail: karpinski@phys.ethz.c [Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich (Switzerland); Zhigadlo, N.D.; Katrych, S.; Bukowski, Z.; Moll, P. [Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich (Switzerland); Weyeneth, S.; Keller, H. [Physik-Institut der Universitaet Zuerich, 8057 Zuerich (Switzerland); Puzniak, R. [Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Tortello, M.; Daghero, D.; Gonnelli, R. [Dipartimento di Fisica, Politecnico di Torino, 10129 Torino (Italy); Maggio-Aprile, I. [DPMC-MaNEP, University of Geneva, Geneva (Switzerland); Fasano, Y. [DPMC-MaNEP, University of Geneva, Geneva (Switzerland); Low Temperatures Laboratory and Instituto Balseiro, Bariloche (Argentina); Fischer, O. [DPMC-MaNEP, University of Geneva, Geneva (Switzerland); Rogacki, K. [Institute of Low Temperature and Structure Research, Polish Academy of Sciences, 50-950 Wroclaw, P.O. Box 1410 (Poland); Batlogg, B. [Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich (Switzerland)


    A review of our investigations on single crystals of LnFeAsO{sub 1-x}F{sub x} (Ln = La, Pr, Nd, Sm, Gd) and Ba{sub 1-x}Rb{sub x}Fe{sub 2}As{sub 2} is presented. A high-pressure technique has been applied for the growth of LnFeAsO{sub 1-x}F{sub x} crystals, while Ba{sub 1-x}Rb{sub x}Fe{sub 2}As{sub 2} crystals were grown using a quartz ampoule method. Single crystals were used for electrical transport, structure, magnetic torque and spectroscopic studies. Investigations of the crystal structure confirmed high structural perfection and show incomplete occupation of the (O, F) position in superconducting LnFeAsO{sub 1-x}F{sub x} crystals. Resistivity measurements on LnFeAsO{sub 1-x}F{sub x} crystals show a significant broadening of the transition in high magnetic fields, whereas the resistive transition in Ba{sub 1-x}Rb{sub x}Fe{sub 2}As{sub 2} simply shifts to lower temperature. The critical current density for both compounds is relatively high and exceeds 2 x 10{sup 9} A/m{sup 2} at 15 K in 7 T. The anisotropy of magnetic penetration depth, measured on LnFeAsO{sub 1-x}F{sub x} crystals by torque magnetometry is temperature dependent and apparently larger than the anisotropy of the upper critical field. Ba{sub 1-x}Rb{sub x}Fe{sub 2}As{sub 2} crystals are electronically significantly less anisotropic. Point-Contact Andreev-Reflection spectroscopy indicates the existence of two energy gaps in LnFeAsO{sub 1-x}F{sub x}. Scanning Tunneling Spectroscopy reveals in addition to a superconducting gap, also some feature at high energy (approx20 meV).

  9. Investigation of an unusual low-temperature phase transformation in RbBH{sub 4} by neutron diffraction

    Kitchen, Brian B. [Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI 48109 (United States); Verdal, Nina, E-mail: [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-6102 (United States); Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742-2115 (United States); Udovic, Terrence J. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-6102 (United States); Rush, John J. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-6102 (United States); Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742-2115 (United States); Hartman, Michael R. [Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI 48109 (United States); DeVries, Daniel J. [Radiation and Isotopes for Health, Delft University of Technology, Mekelweg 15, 2629 JB Delft (Netherlands)


    To investigate the previously reported low-temperature phase transition in rubidium borohydride (RbBH{sub 4}) near 48.5 K, we carried out neutron powder diffraction and vibrational spectroscopy measurements both above and below this temperature on an isotopically-enriched sample of Rb{sup 11}BD{sub 4}. Our diffraction data reflected an average cubic Fm3{sup ¯}m structure with BD{sub 4}{sup −} anion orientational disorder at all temperatures, with no hint of extra Bragg peaks due to long-range orientational order below the transition temperature as reported by others. These structural results and careful analysis of torsional vibrations in RbBD{sub 4} corroborate the results of prior neutron vibrational spectroscopy measurements suggesting that the low-temperature RbBH{sub 4} structure indeed possesses some orientational ordering of the BH{sub 4}{sup −} anions, but of a shorter-ranged nature insensitive to powder diffraction methods. - The neutron powder diffraction pattern of RbBD{sub 4} below the phase transition temperature (shown here in black) is indistinguishable from that collected above the phase transition temperature. The inset depicts the cubic structure that fits the data at both temperatures. - Highlights: • We investigated the nature of the RbBD{sub 4} phase transition using NVS and NPD. • A change in shape of the RbBD{sub 4} torsion mode was observed across the transition. • The RbBD{sub 4} diffraction pattern across this phase transition was unchanged. • The phase transition in RbBD{sub 4} appears to produce only short-range ordering of BD{sub 4}{sup −}.

  10. Loss of Rb proteins causes genomic instability in the absence of mitogenic signaling

    van Harn, Tanja; Foijer, Floris; van Vugt, Marcel; Banerjee, Ruby; Yang, Fentang; Oostra, Anneke; Joenje, Hans; te Riele, Hein


    Loss of G1/S control is a hallmark of cancer, and is often caused by inactivation of the retinoblastoma pathway. However, mouse embryonic fibroblasts lacking the retinoblastoma genes RB1, p107, and p130 (TKO MEFs) are still subject to cell cycle control: Upon mitogen deprivation, they enter and

  11. Structure and chromosomal localization of the human thrombospondin gene.

    Wolf, F W; Eddy, R L; Shows, T B; Dixit, V M


    Thrombospondin (THBS1) is a large modular glycoprotein component of the extracellular matrix and contains a variety of distinct domains, including three repeating subunits (types I, II, and III) that share homology to an assortment of other proteins. Determination of THBS1 gene structure has revealed that the type I repeat modules are encoded by symmetrical exons and that the heparin-binding domain is encoded by a single exon. To further elucidate the higher level organization of THBS1, the gene was localized to the q11-qter region of chromosome 15.

  12. Structural insights into the mechanism of phosphoregulation of the retinoblastoma protein.

    Ekaterina P Lamber

    Full Text Available The retinoblastoma susceptibility protein RB1 is a key regulator of cell proliferation and fate. RB1 operates through nucleating the formation of multi-component protein complexes involved in the regulation of gene transcription, chromatin structure and protein stability. Phosphorylation of RB1 by cyclin-dependent kinases leads to conformational alterations and inactivates the capability of RB1 to bind partner protein. Using small angle X-ray scattering in combination with single particle analysis of transmission electron microscope images of negative-stained material we present the first three-dimensional reconstruction of non-phosphorylated RB1 revealing an extended architecture and deduce the domain arrangement within the molecule. Phosphorylation results in an overt alteration of the molecular shape and dimensions, consistent with the transition to a compact globular architecture. The work presented provides what is to our knowledge the first description of the relative domain arrangement in active RB1 and predicts the molecular movement that leads to RB1 inactivation following protein phosphorylation.

  13. Six novel transition-metal phosphite compounds, with structure related to yavapaiite: Crystal structures and magnetic and thermal properties of A{sup I}[M{sup III}(HPO{sub 3}){sub 2}] (A=K, NH{sub 4}, Rb and M=V, Fe)

    Hamchaoui, Farida [Laboratoire des Sciences des Materiaux, Faculte de Chimie, Universite des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, 16111 Bab-Ezzouar, Alger (Algeria); Alonzo, Veronique [Sciences Chimiques de Rennes, UMR6226, Ecole Nationale Superieure de Chimie de Rennes, CNRS, Avenue du General Leclerc, CS 50837, 35708 Rennes Cedex 7 (France); Universite Europeenne de Bretagne (France); Venegas-Yazigi, Diego [Facultad de Quimia y Biologia, Universitad de Santiago de Chile, USACH, Casilla, 40 Correo 33, Santiago (Chile); Rebbah, Houria [Laboratoire des Sciences des Materiaux, Faculte de Chimie, Universite des Sciences et de la Technologie Houari Boumediene, BP 32 El-Alia, 16111 Bab-Ezzouar, Alger (Algeria); Le Fur, Eric, E-mail: [Sciences Chimiques de Rennes, UMR6226, Ecole Nationale Superieure de Chimie de Rennes, CNRS, Avenue du General Leclerc, CS 50837, 35708 Rennes Cedex 7 (France); Universite Europeenne de Bretagne (France)


    Six new transition metal(III) phosphites A{sup I}[V{sup III}(HPO{sub 3}){sub 2}], where A=K (1), NH{sub 4} (2) and Rb (3) and A{sup I}[Fe{sup III}(HPO{sub 3}){sub 2}] where A=K (4), NH{sub 4} (5) and Rb (6) have been synthesized under hydrothermal conditions and the solid-state structures were solved from single-crystal X-ray diffraction data. These compounds crystallize in the hexagonal system, space group P6{sub 3}mc (no. 186), with a=5.3294(2) A and c=12.3130(5) A for 1, a=5.3330(2) A and c=12.8760(4) A for 2, a=5.3459(2) A and c=12.6850(8) A for 3, a=5.3256(1) A and c=12.2362(3) A for 4, a=5.3229(2) A and c=12.8562(4) A for 5, a=5.3393(2) A and c=12.6913(5) A for 6, with Z=2 in the six phases. The crystal structures of these compounds are isotypic and exhibit a layered structure stacked along the c-axis with the A{sup +} cations located in the interlayer space. The [M{sup III}(HPO{sub 3}){sub 2}]{sup -} sheets are formed by MO{sub 6} octahedra interconnected by HPO{sub 3} tetrahedral phosphite oxoanions through sharing vertices. Thermal analysis shows a large range of stability for compounds containing potassium and rubidium cations with decomposition starting around 550 K for stable compounds and above 840 K for the most stable compounds leading in general to pyrophosphate compounds. Triangular nets of metallic centers are observed within the layers in which antiferromagnetic interactions are evidenced by magnetic susceptibility measurements suggesting magnetic frustration. - Graphical abstract: Six new transition metal(III) phosphites A{sup I}[M{sup III}(HPO{sub 3}){sub 2}], where A=K, NH{sub 4}, Rb and M=V, Fe, have been synthesized. The crystal structures of these compounds are isotypic and exhibit a lamellar structure related to Yavapaiite. The M(HPO{sub 3}){sub 2} layers separated by cationic species present the metallic centers in a triangular arrangement. Bulk antiferromagnetic behavior is observed for all the studied compounds. Highlights: Black

  14. Prediction and analysis of retinoblastoma related genes through gene ontology and KEGG.

    Li, Zhen; Li, Bi-Qing; Jiang, Min; Chen, Lei; Zhang, Jian; Liu, Lin; Huang, Tao


    One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

  15. Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

    Zhen Li


    Full Text Available One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR method followed by incremental feature selection (IFS. 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

  16. LIMD1 is more frequently altered than RB1 in head and neck squamous cell carcinoma: clinical and prognostic implications

    Roy Anup


    Full Text Available Abstract Introduction To understand the role of two interacting proteins LIMD1 and pRB in development of head and neck squamous cell carcinoma (HNSCC, alterations of these genes were analyzed in 25 dysplastic head and neck lesions, 58 primary HNSCC samples and two HNSCC cell lines. Methods Deletions of LIMD1 and RB1 were analyzed along with mutation and promoter methylation analysis of LIMD1. The genotyping of LIMD1 linked microsatellite marker, hmlimD1, was done to find out any risk allele. The mRNA expression of LIMD1 and RB1 were analyzed by Q-PCR. Immunohistochemical analysis of RB1 was performed. Alterations of these genes were correlated with different clinicopathological parameters. Results High frequency [94% (78/83] of LIMD1 alterations was observed in the samples studied. Compare to frequent deletion and methylation, mutation of LIMD1 was increased during tumor progression (P = 0.007. Six novel mutations in exon1 and one novel intron4/exon5 splice-junction mutation were detected in LIMD1 along with a susceptible hmlimD1 (CA20 allele. Some of these mutations [42% (14/33] produced non-functional proteins. RB1 deletion was infrequent (27%. Highly reduced mRNA expression of LIMD1 (25.1 ± 19.04 was seen than RB1 (3.8 ± 8.09, concordant to their molecular alterations. The pRB expression supported this data. Tumors with LIMD1 alterations in tobacco addicted patients without HPV infection showed poor prognosis. Co-alterations of these genes led the worse patients' outcome. Conclusions Our study suggests LIMD1 inactivation as primary event than inactivation of RB1 in HNSCC development.

  17. Proton instability of {sup 73}Rb

    Jokinen, A. [CERN, Geneva (Switzerland). PPE Div.; Oinonen, M. [Univ. of Jyvaeskylae (Finland). Dept. of Physics; Aeystoe, J. [CERN, Geneva (Switzerland). PPE Div.]|[Univ. of Jyvaeskylae (Finland). Dept. of Physics] [and others; ISOLDE Collaboration


    The study of the stability of an astrophysically interesting nucleus {sup 73}Rb was performed by searching its {beta}{sup +} and proton decay at the ISOLDE facility at CERN. Light rubidium isotopes were produced in a spallation reaction of a niobium target induced by a pulsed 1 GeV proton beam. The previously reported proton-unbound character of {sup 73}Rb was confirmed and the upper limit for its production cross-section was reduced by more than one order of magnitude. (orig.)

  18. An RNA interference screen for identifying downstream effectors of the p53 and pRB tumour suppressor pathways involved in senescence

    Ashworth Alan


    Full Text Available Abstract Background Cellular senescence is an irreversible cell cycle arrest that normal cells undergo in response to progressive shortening of telomeres, changes in telomeric structure, oncogene activation or oxidative stress and acts as an important tumour suppressor mechanism. Results To identify the downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways crucial for mediating entry into senescence, we have carried out a loss-of-function RNA interference screen in conditionally immortalised human fibroblasts that can be induced to rapidly undergo senescence, whereas in primary cultures senescence is stochastic and occurs asynchronously. These cells are immortal but undergo a rapid irreversible arrest upon activation of the p53-p21 and p16-pRB pathways that can be readily bypassed upon their inactivation. The primary screen identified 112 known genes including p53 and another 29 shRNAmirs targetting as yet unidentified loci. Comparison of these known targets with genes known to be up-regulated upon senescence in these cells, by micro-array expression profiling, identified 4 common genes TMEM9B, ATXN10, LAYN and LTBP2/3. Direct silencing of these common genes, using lentiviral shRNAmirs, bypassed senescence in the conditionally immortalised cells. Conclusion The senescence bypass screen identified TMEM9B, ATXN10, LAYN and LTBP2/3 as novel downstream effectors of the p53-p21 and p16-pRB tumour suppressor pathways. Although none of them has previously been linked to cellular senescence, TMEM9B has been suggested to be an upstream activator of NF-κB signalling which has been found to have a causal role in promoting senescence. Future studies will focus on determining on how many of the other primary hits also have a casual role in senescence and what is the mechanism of action.

  19. Correlations in the population structure of music, genes and language.

    Brown, Steven; Savage, Patrick E; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A


    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

  20. Detecting Key Structural Features within Highly Recombined Genes

    Wertz, John E; McGregor, Karen F; Bessen, Debra E


    Many microorganisms exhibit high levels of intragenic recombination following horizontal gene transfer events. Furthermore, many microbial genes are subject to strong diversifying selection as part of the pathogenic process. A multiple sequence alignment is an essential starting point for many of the tools that provide fundamental insights on gene structure and evolution, such as phylogenetics; however, an accurate alignment is not always possible to attain. In this study, a new analytic approach was developed in order to better quantify the genetic organization of highly diversified genes whose alleles do not align. This BLAST-based method, denoted BLAST Miner, employs an iterative process that places short segments of highly similar sequence into discrete datasets that are designated “modules.” The relative positions of modules along the length of the genes, and their frequency of occurrence, are used to identify sequence duplications, insertions, and rearrangements. Partial alleles of sof from Streptococcus pyogenes, encoding a surface protein under host immune selection, were analyzed for module content. High-frequency Modules 6 and 13 were identified and examined in depth. Nucleotide sequences corresponding to both modules contain numerous duplications and inverted repeats, whereby many codons form palindromic pairs. Combined with evidence for a strong codon usage bias, data suggest that Module 6 and 13 sequences are under selection to preserve their nucleic acid secondary structure. The concentration of overlapping tandem and inverted repeats within a small region of DNA is highly suggestive of a mechanistic role for Module 6 and 13 sequences in promoting aberrant recombination. Analysis of pbp2X alleles from Streptococcus pneumoniae, encoding cell wall enzymes that confer antibiotic resistance, supports the broad applicability of this tool in deciphering the genetic organization of highly recombined genes. BLAST Miner shares with phylogenetics the

  1. p107 in the public eye: an Rb understudy and more

    Wirt Stacey E


    Full Text Available Abstract p107 and its related family members Rb and p130 are critical regulators of cellular proliferation and tumorigenesis. Due to the extent of functional overlap within the Rb family, it has been difficult to assess which functions are exclusive to individual members and which are shared. Like its family members, p107 can bind a variety of cellular proteins to affect the expression of many target genes during cell cycle progression. Unlike Rb and p130, p107 is most highly expressed during the G1 to S phase transition of the cell cycle in actively dividing cells and accumulating evidence suggests a role for p107 during DNA replication. The specific roles for p107 during differentiation and development are less clear, although emerging studies suggest that it can cooperate with other Rb family members to control differentiation in multiple cell lineages. As a tumor suppressor, p107 is not as potent as Rb, yet studies in knockout mice have revealed some tumor suppressor functions in mice, depending on the context. In this review, we identify the unique and overlapping functions of p107 during the cell cycle, differentiation, and tumorigenesis.

  2. Human estrogen sulfotransferase gene (STE): Cloning, structure, and chromosomal localization

    Her, Chengtao; Aksoy, I.A.; Weinshilboum, M. [Mayo Foundation, Rochester, MI (United States)] [and others


    Sulfation is an important pathway in the metabolism of estrogens. We recently cloned a human liver estrogen sulfotransferase (EST) cDNA. We have now determined the structure and chromosomal localization of the EST gene, STE, as a step toward molecular genetic studies of the regulation of EST in humans. STE spans approximately 20 kb and consists of 8 exons, ranging in length from 95 to 181 bp. The locations of most exon-intron splice junctions within STE are identical to those found in a human phenol ST (PST) gene, STM, and in a rat PST gene. In addition, the locations of five STE introns are also conserved in the human dehydroepiandrosterone (DBEA) ST gene, STD. The 5{prime} flanking region of STE contains one CCAAT and two TATA sequences. The location of one of the TATA box elements is in excellent agreement with the site of transcription initiation as determined by 5{prime}-rapid amplification of cDNA ends. STE was mapped to human chromosome 4q13.1 by fluorescence in situ hybridization. Cloning and structural characterization of STE will now make it possible to study potential molecular genetic mechanisms involved in the regulation of EST in human tissues. 50 refs., 6 figs., 1 tab.

  3. Rich structural chemistry in new alkali metal yttrium tellurites: three-dimensional frameworks of NaYTe4O10, KY(TeO3)2, RbY(TeO3)2, and a novel variant of hexagonal tungsten bronze, CsYTe3O8.

    Kim, Youngkwon; Lee, Dong Woo; Ok, Kang Min


    Pure polycrystalline phases and single crystals of four new quaternary alkali metal yttrium tellurites, NaYTe4O10, KY(TeO3)2, RbY(TeO3)2, and CsYTe3O8, have been prepared by solid-state and hydrothermal reactions using A2CO3 (A = Na, K, Rb, and Cs), Y(NO3)3·6H2O, Y2O3, and TeO2 as starting reagents. X-ray diffraction analyses suggest that NaYTe4O10 exhibits a highly symmetric three-dimensional (3D) framework consisting of YO8 square antiprisms and chains of TeO4 polyhedra. Within the framework, six- (6-) and eight-membered ring (8-MR) channels are observed. KY(TeO3)2 and RbY(TeO3)2 are isostructural to each other and reveal another 3D framework with structures containing YO6 octahedra and TeO3 trigonal pyramids with 4-MR and 12-MR channels. CsYTe3O8 shows a hexagonal tungsten bronze (HTB)-like topology composed of hexagonal tungsten oxide-like layers of TeO4 polyhedra and YO6 octahedral linkers with 3-MR and 6-MR channels. Thermal analyses, elemental analyses, and spectroscopic characterizations, such as UV-vis diffuse reflectance and infrared spectra, are presented, as are local dipole moment calculations for the constituent asymmetric polyhedra TeO3 and TeO4.

  4. Analysis of ribosomal protein gene structures: implications for intron evolution.


    Full Text Available Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs and mitochondrial ribosomal proteins (MRPs, which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be "conserved," i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.

  5. [Insect antimicrobial peptides: structures, properties and gene regulation].

    Wang, Yi-Peng; Lai, Ren


    Insect antimicrobial peptides (AMPs) are an important group of insect innate immunity effectors. Insect AMPs are cationic and contain less than 100 amino acid residues. According to structure, insect AMPs can be divided into a limited number of families. The diverse antimicrobial spectrum of insect AMPs may indicate different modes of action. Research on the model organism Drosophila indicate that insect AMPs gene regulation involves multiple signaling pathways and a large number of signaling molecules.

  6. RB1CC1 activates RB1 pathway and inhibits proliferation and cologenic survival in human cancer.

    Tokuhiro Chano

    Full Text Available RB1-inducible coiled-coil 1 (RB1CC1, also known as FIP200 plays a role in the enhancement of the RB1 pathway through the direct binding to a GC-rich region 201bp upstream (from the initiation ATG of the RB1 promoter. Here, we identified hSNF5 and p53 as the binding partners of RB1CC1 by immunoprecipitation and immunofluorescence assays. Interaction between these molecules and the RB1 pathway was analyzed by the assays of chromatin immunoprecipitation, luciferase-reporter, reverse transcription-polymerase chain reaction and immunoblot. The tumor growth suppression by RB1CC1 was evaluated by flow cytometry or by a cell growth assay. The nuclear RB1CC1 complex involving hSNF5 and/or p53 activated transcription of RB1, p16 and p21, and suppressed tumor cell growth. Furthermore, nuclear RB1CC1 expression significantly correlated with those of RB1 and p16 in breast cancer tissue in vivo, and the Ki-67 proliferation index was dependent on p53 as well as RB1CC1. The present study indicates that RB1CC1 together with hSNF5 and/or p53 enhances the RB1 pathway through transcriptional activation of RB1, p16 and p21. Evaluation of RB1CC1 expression combined with RB1 and p53 status is expected to provide useful information in clinical practice and future therapeutic strategies in breast cancer.

  7. RGS16, a novel p53 and pRb cross-talk candidate inhibits migration and invasion of pancreatic cancer cells.

    Carper, Miranda B; Denvir, James; Boskovic, Goran; Primerano, Donald A; Claudio, Pier Paolo


    Data collected since the discovery of p53 and pRb/RB1 suggests these tumor suppressors cooperate to inhibit tumor progression. Patients who have mutations in both p53 and RB1 genes have increased tumor reoccurrence and decreased survival compared to patients with only one tumor suppressor gene inactivated. It remains unclear how p53 and pRb cooperate toward inhibiting tumorigenesis. Using RNA expression profiling we identified 179 p53 and pRb cross-talk candidates in normal lung fibroblasts (WI38) cells exogenously coexpressing p53 and pRb. Regulator of G protein signaling 16 (RGS16) was among the p53 and pRb cross-talk candidates and has been implicated in inhibiting activation of several oncogenic pathways associated with proliferation, migration, and invasion of cancer cells. RGS16 has been found to be downregulated in pancreatic cancer patients with metastases compared to patients without metastasis. Expression of RGS16 mRNA was decreased in the pancreatic cancer cell lines tested compared to control. Expression of RGS16 inhibited migration of the BxPC-3 and AsPC-1 but not PANC-1 cells and inhibited invasion of BxPC-3 and AsPC-1 cells with no impact on cell viability. We have identified for the first time p53 and pRb cross-talk candidates and a role for RGS16 to inhibit pancreatic cancer migration and invasion.

  8. The gene structure of the Drosophila melanogaster proto-oncogene, kayak, and its nested gene, fos-intronic gene.

    Hudson, Stephanie Gidget; Goldstein, Elliott S


    We present herein a new model for the structure of the Drosophila kayak gene as well as preliminary data on the functional differences of its various isoforms. kayak is a homolog of the human proto-oncogene, c-fos. kayak has three different starts of transcription, and therefore promoters (P)kay-alpha, (P)kay-beta and (P)kay-gamma. These three promoters lead to four different transcripts: kay-alpha, kay(sro), kay-beta and kay-gamma. (P)kay-alpha produces two different transcripts: kay-alpha and kay(sro) where the other two promoters, (P)kay-beta and (P)kay-gamma, produce a single transcript each. The transcripts kay-alpha, beta and gamma all splice into the mainbody of the kay gene, which codes for the DNA binding domain and leucine zipper; kay(sro) is not spliced. Also, within this region is a nested gene, fos-intronic gene (fig) which is transcribed in the opposite direction. fig codes for a predicted PP2C phosphatase. fig has two different promoters which produce two different transcripts, both in the same reading frame, fig-alpha and beta. This is an unusual gene structure for Drosophila. Only 13% of Drosophila genes have multiple promoters and only 7% have a nested gene. RT-PCR was performed on each transcript to determine the relative amounts of each RNA produced. All spliced kay transcripts appear to have equal abundance. The unspliced kay(sro) transcript has a lower abundance than kay-alpha. Both fig transcripts are also detected in all stages tested. Lethal phase analysis and complementation testing suggest that the three isoforms of kayak may have different functions.

  9. Disruption of Rb/E2F pathway results in increased cyclooxygenase-2 expression and activity in prostate epithelial cells.

    Davis, Joanne N; McCabe, Michael T; Hayward, Simon W; Park, John M; Day, Mark L


    The loss of the retinoblastoma tumor suppressor gene (RB) is common in many human cancers, including prostate. We previously reported that engineered deletion of RB in prostate epithelial cells results in sustained cell growth in serum-free media, a predisposition to develop hyperplasia and dysplasia in prostate tissue recombinant grafts, and sensitization to hormonal carcinogenesis. Examining the molecular consequence of RB loss in this system, we show that cyclooxygenase-2 (COX-2) is significantly up-regulated following RB deletion in prostate tissue recombinants. To study the effect of RB deletion on COX-2 regulation, we generated wild-type (PrE) and Rb-/- (Rb-/-PrE) prostate epithelial cell lines rescued by tissue recombination. We show elevated COX-2 mRNA and protein expression in Rb-/-PrE cell lines with increased prostaglandin synthesis. We also find that loss of Rb leads to deregulated E2F activity, with increased expression of E2F target genes, and that exogenous expression of E2F1 results in elevated COX-2 mRNA and protein levels. COX-2 promoter studies reveal that E2F1 transcriptionally activates COX-2, which is dependent on the transactivation and DNA-binding domains of E2F1. Further analysis revealed that the E2F1 target gene, c-myb, is elevated in Rb-/-PrE cells and E2F1-overexpressing cells, whereas ectopic overexpression of c-myb activates the COX-2 promoter in prostate epithelial cells. Additionally, cotransfection with E2F1 and a dominant-negative c-myb inhibited E2F1 activation of the COX-2 promoter. Taken together, these results suggest activation of a transcriptional cascade by which E2F1 regulates COX-2 expression through the c-myb oncogene. This study reports a novel finding describing that deregulation of the Rb/E2F complex results in increased COX-2 expression and activity.

  10. Functional Inactivation of pRB Results in Aneuploid Mammalian Cells After Release From a Mitotic Block

    Laura Lentini


    Full Text Available The widespread chromosome instability observed in tumors and in early stage carcinomas suggests that aneuploidy could be a prerequisite for cellular transformation and tumor initiation. Defects in tumor suppressers and genes that are part of mitotic checkpoints are likely candidates for the aneuploid phenotype. By using flow cytometric, cytogenetic, immunocytochemistry techniques we investigated whether pRB deficiency could drive perpetual aneuploidy in normal human and mouse fibroblasts after mitotic checkpoint challenge by microtubule-destabilizing drugs. Both mouse and human pRB-deficient primary fibroblasts resulted, upon release from a mitotic block, in proliferating aneuploid cells possessing supernumerary centrosomes. Aneuploid pRB-deficient cells show an elevated variation in chromosome numbers among cells of the same clone. In addition, these cells acquired the capability to grow in an anchorage-independent way at the same extent as tumor cells did suggesting aneuploidy as an initial mutational step in cell transformation. Normal Mouse Embryonic Fibroblasts. (MEFs harboring LoxP sites flanking exon 19 of the Rb gene arrested in G2/M with duplicated centrosomes after colcemid treatment. However, these cells escaped the arrest and became aneuploid upon pRB ablation by CRE recombinase, suggesting pRB as a major component of a checkpoint that controls cellular ploidy.

  11. Doing Business Economy Profile 2015 : Venezuela, RB


    This economy profile for Doing Business 2015 presents the 11 Doing Business indicators for Venezuela RB. To allow for useful comparison, the profile also provides data for other selected economies (comparator economies) for each indicator. Doing Business 2015 is the 12th edition in a series of annual reports measuring the regulations that enhance business activity and those that constrain ...

  12. Progress of the ~(87)Rb Fountain Clock

    ZHOU Zi-Chao; WEI Rong; SHI Chun-Yan; LV De-Sheng; LI Tang; WANG Yu-Zhu


    A fountain atomic clock based on cold ~(87)Rb atoms has been in operation in our laboratory for several months.We therefore report the design of the rubidium fountain clock including its physical package,optical system and daily operation.Ramsey fringes have been attained with the signal to noise ratio of about 100.

  13. The experiment on the saturation polarization of Rb vapour

    Huang Xiang-You; You Pei-Lin; Du Wei-Min


    @@ A cylindrical capacitor containing rubidium vapour is made. The capacitance of it at. different voltages is measured under a certain Rb vapour pressure. The experimental C-V curve shows that the saturation polarization of Rb vapour is easily observed. The experiment further supports the idea that the Rb atom has a large permanent electric dipole moment.

  14. Overexpression of two penicillin structural genes in Aspergillus nidulans.

    Fernández-Cañón, J M; Peñalva, M A


    We have placed two different penicillin structural genes from Aspergillus nidulans, ipnA (encoding isopenicillin N synthetase, IPNS) and acyA (encoding acyl-CoA:6-aminopenicillanic acid acyltransferase, AAT), under the control of the strong alcA promoter [alcA(p)]. Single copies of these transcriptional fusions were targeted to the same chromosomal location and conditions have been worked out which simultaneously allow induction of the alcA(p) and support penicillin biosynthesis. Transcriptional induction of the chimeric genes alcA(p)::ipnA or alcA(p)::acyA(cdna) in the relevant recombinant strains results in 10-fold higher levels of the ipnA or acyA transcripts than those resulting from transcription of the corresponding endogenous genes. This increase causes a 40-fold rise in IPNS activity or a 8-fold rise in AAT activity. Despite this rise in enzyme levels, forced expression of the ipnA gene results in only a modest increase in levels of exported penicillin, whereas forced expression of the acyA gene reduces penicillin production, showing that neither of these enzymes is rate-limiting for penicillin biosynthesis in A. nidulans. A genomic version of the alcA(p)::acyA fusion in which the acyA gene is interrupted by three small introns, is inducible by threonine to a lesser extent (as determined by both acyA mRNA levels and AAT enzyme levels) than the corresponding cDNA version, suggesting that processing of the introns present in the primary transcript may limit acyA expression.

  15. Structures and Boolean Dynamics in Gene Regulatory Networks

    Szedlak, Anthony

    This dissertation discusses the topological and dynamical properties of GRNs in cancer, and is divided into four main chapters. First, the basic tools of modern complex network theory are introduced. These traditional tools as well as those developed by myself (set efficiency, interset efficiency, and nested communities) are crucial for understanding the intricate topological properties of GRNs, and later chapters recall these concepts. Second, the biology of gene regulation is discussed, and a method for disease-specific GRN reconstruction developed by our collaboration is presented. This complements the traditional exhaustive experimental approach of building GRNs edge-by-edge by quickly inferring the existence of as of yet undiscovered edges using correlations across sets of gene expression data. This method also provides insight into the distribution of common mutations across GRNs. Third, I demonstrate that the structures present in these reconstructed networks are strongly related to the evolutionary histories of their constituent genes. Investigation of how the forces of evolution shaped the topology of GRNs in multicellular organisms by growing outward from a core of ancient, conserved genes can shed light upon the ''reverse evolution'' of normal cells into unicellular-like cancer states. Next, I simulate the dynamics of the GRNs of cancer cells using the Hopfield model, an infinite range spin-glass model designed with the ability to encode Boolean data as attractor states. This attractor-driven approach facilitates the integration of gene expression data into predictive mathematical models. Perturbations representing therapeutic interventions are applied to sets of genes, and the resulting deviations from their attractor states are recorded, suggesting new potential drug targets for experimentation. Finally, I extend the Hopfield model to modular networks, cyclic attractors, and complex attractors, and apply these concepts to simulations of the cell cycle

  16. The pRB-related protein p107 contains two growth suppression domains : independent interactions with E2F and cyclin/cdk complexes

    Zhu, L.; Enders, G.; Lees, J.A.; Beijersbergen, R.L.; Bernards, R.A.; Harlow, E.


    Unregulated expression of either the retinoblastoma protein (pRB) or the related protein p107 can cause growth arrest of sensitive cells in the G1 phase of the cell cycle. However, growth arrests mediated by p107 and pRB are not identical. Through structure-function and co-expression analyses we hav

  17. Polyubiquitin gene expression and structural properties of the ubi4-2 gene in Petroselinum crispum.

    Kawalleck, P; Somssich, I E; Feldbrügge, M; Hahlbrock, K; Weisshaar, B


    Ubiquitin is an omnipresent protein found in all eukaryotes so far analysed. It is involved in several important processes, including protein turnover, chromosome structure and stress response. Parsley (Petroselinum crispum) contains at least two active polyubiquitin (ubi4) genes encoding hexameric precursor proteins. The deduced amino acid sequences of the ubiquitin monomers are identical to one another and to ubiquitin sequences from several other plant species. Analysis of the promoter region of one ubi4 gene revealed putative regulatory elements. In parsley plants, the ubi4 mRNAs were the predominant ubiquitin mRNAs and were present at comparable levels in all plant organs tested. In cultured parsley cells, high levels of ubiquitin gene expression remained unaffected by heat shock, elicitor or light treatment.

  18. Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight

    Wielgus Susan M


    Full Text Available Abstract Background Late blight is the most serious potato disease world-wide. The most effective and environmentally sound way for controlling late blight is to incorporate natural resistance into potato cultivars. Several late blight resistance genes have been cloned recently. However, there is almost no information available about the resistance pathways mediated by any of those genes. Results We previously cloned a late blight resistance gene, RB, from a diploid wild potato species Solanum bulbocastanum. Transgenic potato lines containing a single RB gene showed a rate-limiting resistance against all known races of Phytophthora infestans, the late blight pathogen. To better understand the RB-mediated resistance we silenced the potato Rar1 and Sgt1 genes that have been implicated in mediating disease resistance responses against various plant pathogens and pests. The Rar1 and Sgt1 genes of a RB-containing potato clone were silenced using a RNA interference (RNAi-based approach. All of the silenced potato plants displayed phenotypically normal growth. The late blight resistance of the Rar1 and Sgt1 silenced lines were evaluated by a traditional greenhouse inoculation method and quantified using a GFP-tagged P. infestans strain. The resistance of the Rar1-silenced plants was not affected. However, silencing of the Sgt1 gene abolished the RB-mediated resistance. Conclusion Our study shows that silencing of the Sgt1 gene in potato does not result in lethality. However, the Sgt1 gene is essential for the RB-mediated late blight resistance. In contrast, the Rar1 gene is not required for RB-mediated resistance. These results provide additional evidence for the universal role of the Sgt1 gene in various R gene-mediated plant defense responses.

  19. Linking stochastic fluctuations in chromatin structure and gene expression.

    Christopher R Brown

    Full Text Available The number of mRNA and protein molecules expressed from a single gene molecule fluctuates over time. These fluctuations have been attributed, in part, to the random transitioning of promoters between transcriptionally active and inactive states, causing transcription to occur in bursts. However, the molecular basis of transcriptional bursting remains poorly understood. By electron microscopy of single PHO5 gene molecules from yeast, we show that the "activated" promoter assumes alternative nucleosome configurations at steady state, including the maximally repressive, fully nucleosomal, and the maximally non-repressive, nucleosome-free, configuration. We demonstrate that the observed probabilities of promoter nucleosome configurations are obtained from a simple, intrinsically stochastic process of nucleosome assembly, disassembly, and position-specific sliding; and we show that gene expression and promoter nucleosome configuration can be mechanistically coupled, relating promoter nucleosome dynamics and gene expression fluctuations. Together, our findings suggest a structural basis for transcriptional bursting, and offer new insights into the mechanism of transcriptional regulation and the kinetics of promoter nucleosome transitions.

  20. Alternative RNA Structure-Coupled Gene Regulations in Tumorigenesis

    Feng-Chi Chen


    Full Text Available Alternative RNA structures (ARSs, or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.

  1. Cholera toxin structure, gene regulation and pathophysiological and immunological aspects.

    Sánchez, J; Holmgren, J


    Many notions regarding the function, structure and regulation of cholera toxin expression have remained essentially unaltered in the last 15 years. At the same time, recent findings have generated additional perspectives. For example, the cholera toxin genes are now known to be carried by a non-lytic bacteriophage, a previously unsuspected condition. Understanding of how the expression of cholera toxin genes is controlled by the bacterium at the molecular level has advanced significantly and relationships with cell-density-associated (quorum-sensing) responses have recently been discovered. Regarding the cell intoxication process, the mode of entry and intracellular transport of cholera toxin are becoming clearer. In the immunological field, the strong oral immunogenicity of the non-toxic B subunit of cholera toxin (CTB) has been exploited in the development of a now widely licensed oral cholera vaccine. Additionally, CTB has been shown to induce tolerance against co-administered (linked) foreign antigens in some autoimmune and allergic diseases.

  2. Improved tests of Local Position Invariance using 87Rb and 133Cs fountains

    Guéna, Jocelyne; Rovera, Daniele; Rosenbusch, Peter; Tobar, Michael E; Laurent, Philippe; Clairon, André; Bize, Sébastien


    We report tests of Local Position Invariance (LPI) based on measurements of the ratio of the ground state hyperfine frequencies of 133Cs and 87Rb in laser-cooled atomic fountain clocks. Measurements extending over 14 years set a stringent limit to a possible variation with time of this ratio: d ln(nu_Rb/nu_Cs)/dt=(-1.39 +/- 0.91)x 10-16 yr-1. This improves by a factor of 7.7 over our previous report (H. Marion et al.}, Phys. Rev. Lett. 90, 150801 (2003)). Our measurements also set the first limit to a fractional variation of the Rb/Cs ratio with gravitational potential at the level of c^2 d ln(nu_Rb/nu_Cs)/dU=(0.11 +/- 1.04)x 10^-6, providing a new stringent differential redshift test. The above limits equivalently apply to the fractional variation of the quantity alpha^{-0.49}x(g_Rb/g_Cs), which involves the fine structure constant alpha and the ratio of the nuclear g-factors of the two alkalis. The link with variations of the light quark mass is also presented together with a global analysis combining with ...

  3. Upper Bound to the Ionization Energy of 85Rb2

    Bellos, M A; Banerjee, J; Ascoli, M; Allouche, A -R; Eyler, E E; Gould, P L; Stwalley, W C


    We report an upper bound to the ionization energy of 85Rb2 of 31348.0(6) cm-1, which also provides a lower bound to the dissociation energy D0 of 85Rb2+ of 6307.5(6) cm-1. These bounds were measured by the onset of autoionization of excited states of 85Rb2 below the 5s+7p atomic limit. We form 85Rb2 molecules via photoassociation of ultracold 85Rb atoms, and subsequently excite the molecules by single-photon ultraviolet transitions to states above the ionization threshold.


    Ahyar Ahmad


    Full Text Available In this study, we cloned and sequenced cDNA encoding the chicken p46 polypeptide, RbAp46. The cDNA encoding a protein consists of 424 amino acids is a member of the WD protein family, with seven WD repeat motifs, and exhibits 90.3% identity to RbAp48, and 94.3% identity to the human RbAp46. The RbAp46 fusion protein were synthesized by in vitro translation system and in Escherichia coli under induction by 50 µM IPTG and single step purified with glutathione-Agarose beads, showed that GST-tagged protein of approximately 72 kDa. The in vitro experiment established that RbAp46 interacts with chicken histones, chHDAC-1, and chHAT-1. The in vitro immunoprecipitation experiment, involving truncated mutants of RbAp46, revealed not only that two regions comprising amino acids 33-179 and 375-404 are necessary for its binding to H2B, but also that two regions comprising amino acids 1-32 and 405-424 are necessary for its binding to H4. Furthermore, the GST pulldown affinity assay, involving truncated mutants of RbAp46, revealed that a region comprising amino acids 359-404 binds to chHAT-1 in vitro. Taken together, these results indicate not only that RbAp46 should participate differentially in a number of DNA-utilizing processes through interactions of its distinct regions with histones and chHAT-1, but also that the proper propeller structure of RbAp46 is not necessary for its interaction with chHAT-1.

  5. 76 FR 24798 - Airworthiness Directives; Rolls-Royce plc (RR) RB211-Trent 875-17, RB211-Trent 877-17, RB211...


    ...-30-AD; Amendment 39-16657; AD 2011-08-07] RIN 2120-AA64 Airworthiness Directives; Rolls-Royce plc (RR... 2. The FAA amends Sec. 39.13 by adding the following new AD: 2011-08-07 Rolls-Royce plc: Amendment... applies to Rolls-Royce plc (RR) RB211-Trent 875-17, RB211-Trent 877-17, RB211-Trent 884-17,...

  6. Preparation and Photoemission Spectra of Rb3C60 Single-Crystal Thin Films

    李宏年; 吴太权; 陈晓; 李海洋; 鲍世宁; 徐亚伯; 钱海杰; 易卜拉欣奎热西; 刘风琴


    Rb3 C60 single-crystal thin films were prepared on the cleaved (111) surface of C60 single crystal. The photoemission spectrum line shapes of the lowest unoccupied molecular orbital (LUMO) derived band at room temperature and 150K were established by synchrotron radiation photoemission spectrum measurements. The density of states near the Fermi level was distinctly affected by temperature. No less than six sub-peaks of the LUMOband were observed even at room temperature. The existence of so many sub-peaks offered the opportunities to analyse in more detail the orientational structure and the electron-Boson interactions of the narrow-band metallic Rb3 C60 .

  7. Bloch oscillations of ultracold atoms: a tool for a metrological determination of h/m Rb.

    Battesti, Rémy; Cladé, Pierre; Guellati-Khélifa, Saïda; Schwob, Catherine; Grémaud, Benoît; Nez, François; Julien, Lucile; Biraben, François


    We use Bloch oscillations in a horizontal moving standing wave to transfer a large number of photon recoils to atoms with a high efficiency (99.5% per cycle). By measuring the photon recoil of 87Rb, using velocity-selective Raman transitions to select a subrecoil velocity class and to measure the final accelerated velocity class, we have determined h/m(Rb) with a relative precision of 0.4 ppm. To exploit the high momentum transfer efficiency of our method, we are developing a vertical standing wave setup. This will allow us to measure h/m(Rb) better than 10(-8) and hence the fine structure constant alpha with an uncertainty close to the most accurate value coming from the (g-2) determination.

  8. Formation of ultracold metastable RbCs molecules by short-range photoassociation

    Gabbanini, C


    Ultracold metastable RbCs molecules are observed in a double species MOT through photoassociation near the Rb(5S$_{1/2}$)+Cs(6P$_{3/2}$) dissociation limit followed by radiative stabilization. The molecules are formed in their lowest triplet electronic state and are detected by resonant enhanced two-photon ionization through the previously unobserved $(3)^{3}\\Pi \\leftarrow a^{3}\\Sigma^{+}$ band. The large rotational structure of the observed photoassociation lines is assigned to the lowest vibrational levels of the $0^+,0^-$ excited states correlated to the Rb(5P$_{1/2}$)+Cs(6S$_{1/2}$) dissociation limit. This demonstrates the possibility to induce direct photoassociation in heteronuclear alkali-metal molecules at short internuclear distance, as pointed out in [J. Deiglmayr \\textit{et al.}, Phys. Rev. Lett. \\textbf{101}, 13304 (2008)].

  9. Xenoestrogenic gene expression: structural features of active polycyclic aromatic hydrocarbons.

    Schultz, T Wayne; Sinks, Glendon D


    Estrogenicity was assessed using the Saccharomyces cerevisiae-based Lac-Z reporter assay and was reported as the logarithm of the inverse of the 50% molar beta-galactosidase activity (log[EC50(-1)]). In an effort to quantify the relationship between molecular structure of polycyclic aromatic hydrocarbons (PAHs) and estrogenic gene expression, a series of PAHs were evaluated. With noted exceptions, the results of these studies indicate that the initial two-dimensional structural warning for estrogenicity, the superpositioning of a hydroxylated aromatic system on the phenolic A-ring of 17-beta-estradiol, can be extended to the PAHs. This two-dimensional-alignment criterion correctly identified estrogenicity of 22 of the 29 PAHs evaluated. Moreover, the estrogenic potency of these compounds was directly related to the size of the hydrophobic backbone. The seven compounds classified incorrectly by this structural feature were either dihydroxylated naphthalenes or aromatic nitrogen-heterocyclic compounds; all such compounds were false positives. Results with dihydroxylated naphthalenes reveal derivatives that were nonestrogenic when superimposed on the phenolic A-ring of 17-beta-estradiol had the second hydroxyl group in the position of the C-ring or were catechol-like in structure. Structural alerts for nitrogen-heterocyclic compounds must take into account the position of the hydroxyl group and the in-ring nitrogen atom; compounds with the hydroxyl group and nitrogen atom involved with the same ring were observed to be nonactive.

  10. RB4CD12 epitope expression and heparan sulfate disaccharide composition in brain vasculature

    Hosono-Fukao, T.; Ohtake-Niimi, S.; Nishitsuji, K.; Hossain, M.M.; Kuppevelt, A.H.M.S.M. van; Michikawa, M.; Uchimura, K.


    RB4CD12 is a phage display antibody that recognizes a heparan sulfate (HS) glycosaminoglycan epitope. The epitope structure is proposed to contain a trisulfated disaccharide, [-IdoA(2-OSO(3))-GlcNSO(3) (6-OSO(3))-], which supports HS binding to various macromolecules such as growth factors and cytok

  11. Deficiency of G1 regulators P53, P21Cip1 and/or pRb decreases hepatocyte sensitivity to TGFβ cell cycle arrest

    Harrison David J


    Full Text Available Abstract Background TGFβ is critical to control hepatocyte proliferation by inducing G1-growth arrest through multiple pathways leading to inhibition of E2F transcription activity. The retinoblastoma protein pRb is a key controller of E2F activity and G1/S transition which can be inhibited in viral hepatitis. It is not known whether the impairment of pRb would alter the growth inhibitory potential of TGFβ in disease. We asked how Rb-deficiency would affect responses to TGFβ-induced cell cycle arrest. Results Primary hepatocytes isolated from Rb-floxed mice were infected with an adenovirus expressing CRE-recombinase to delete the Rb gene. In control cells treatment with TGFβ prevented cells to enter S phase via decreased cMYC activity, activation of P16INK4A and P21Cip and reduction of E2F activity. In Rb-null hepatocytes, cMYC activity decreased slightly but P16INK4A was not activated and the great majority of cells continued cycling. Rb is therefore central to TGFβ-induced cell cycle arrest in hepatocytes. However some Rb-null hepatocytes remained sensitive to TGFβ-induced cell cycle arrest. As these hepatocytes expressed very high levels of P21Cip1 and P53 we investigated whether these proteins regulate pRb-independent signaling to cell cycle arrest by evaluating the consequences of disruption of p53 and p21Cip1. Hepatocytes deficient in p53 or p21Cip1 showed diminished growth inhibition by TGFβ. Double deficiency had a similar impact showing that in cells containing functional pRb; P21Cip and P53 work through the same pathway to regulate G1/S in response to TGFβ. In Rb-deficient cells however, p53 but not p21Cip deficiency had an additive effect highlighting a pRb-independent-P53-dependent effector pathway of inhibition of E2F activity. Conclusion The present results show that otherwise genetically normal hepatocytes with disabled p53, p21Cip1 or Rb genes respond less well to the antiproliferative effects of TGFβ. As the function of

  12. miR-449a enhances radiosensitivity through modulating pRb/E2F1 in prostate cancer cells.

    Mao, Aihong; Liu, Yang; Wang, Yali; Zhao, Qiuyue; Zhou, Xin; Sun, Chao; Di, Cuixia; Si, Jing; Gan, Lu; Zhang, Hong


    miR-449a, a novel tumor suppressor, is deregulated in various malignancies, including prostate cancer. Overexpression of miR-449a induces cell cycle arrest, apoptosis, and senescence, but its role in response to ionizing radiation and underlying molecular mechanism are still unknown. Here, we report that miR-449a enhances radiation-induced G2/M phase arrest and apoptosis through modulating pRb/E2F1 and sensitizes prostate cancer cells to X-ray radiation. In wild-type Rb PC-3 cells, overexpression of miR-449a enhances radiation-induced G2/M arrest and apoptosis and promotes the sensitivity to X-ray radiation. While mutant Rb DU-145 cells are resistant to the X-ray radiation despite in the presence of miR-449a. The cell cycle distribution of DU-145 cells is not significantly altered by miR-449a in the response to ionizing radiation. Furthermore, elevated miR-449a downregulates cell cycle regulator CDC25A and oncogene HDAC1. By targeting genes involved in controlling pRb/E2F1 activity, miR-449a regulates cell cycle progression and apoptosis and consequently enhances the radiosensitivity of PC-3 cells. Thus, miR-449a, as a miRNA component of the Rb pathway, promotes the radiosensitivity of PC-3 cells through regulating pRb/E2F1.

  13. Structure determination of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, NaLaS2 and crystal-chemical analysis of the group 1 and thallium(I) rare-earth sulfide series.

    Fábry, Jan; Havlák, Lubomír; Dušek, Michal; Vaněk, Přemysl; Drahokoupil, Jan; Jurek, Karel


    One of the purposes of this work is to provide a crystallographic review of group 1 and thallium rare-earth ternary sulfides M(+)Ln(3+)S2. We have therefore determined crystal structures of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, which belong to the α-NaFeO2 structural family (R3m), as well as NaLaS2, which is derived from the disordered NaCl structural type (Fm3m). The determined structures were compared with known members of the group 1 as well as thallium(I) rare-earth sulfides by the standard tools of crystal-chemical analysis such as comparison of bond-valences, analysis of interatomic distances and comparison of the unit-cell parameters. The results indicate why the cubic structural type is limited to Li(+) and Na(+) members of the series only. The analysis has also revealed frequent problems in the reported crystal structures, especially in the determination of the K(+) compounds, probably due to severe absorption and different accuracy and sensitivity of various instruments. Intense diffuse scattering has been discovered in NaLaS2, which will be the subject of further investigation. The newly determined as well as already known structures are summarized, together with critical comments about possible errors in the previous structure determinations.

  14. Three Magnetic Rotation Bands in 84^Rb

    Shen, Shuifa; Han, Guangbing; Wen, Shuxian; Yan, Yupeng; Wu, Xiaoguang; Zhu, Lihua; He, Chuangye; Li, Guangsheng


    High-spin states in $^{84}$Rb are studied by using the $^{70}$Zn($^{18}$O, p3n)$^{84}$Rb reaction at beam energy of 75 MeV. Three high-lying negative-parity bands are established, whose level spacings are very regular, i.e., there don't exist signature splitting. The dipole character of the transitions of these three bands is assigned by the $\\gamma$-$\\gamma$ directional correlations of oriented states (DCO) intensity ratios and the multipolarity M1 is suggested by the analogy to multiparticle excitations in neighboring nuclei. The strong M1 and weak or no E2 transitions are observed. All these characteristic features show they are magnetic rotation bands.

  15. Recognizing genes and other components of genomic structure

    Burks, C. (Los Alamos National Lab., NM (USA)); Myers, E. (Arizona Univ., Tucson, AZ (USA). Dept. of Computer Science); Stormo, G.D. (Colorado Univ., Boulder, CO (USA). Dept. of Molecular, Cellular and Developmental Biology)


    The Aspen Center for Physics (ACP) sponsored a three-week workshop, with 26 scientists participating, from 28 May to 15 June, 1990. The workshop, entitled Recognizing Genes and Other Components of Genomic Structure, focussed on discussion of current needs and future strategies for developing the ability to identify and predict the presence of complex functional units on sequenced, but otherwise uncharacterized, genomic DNA. We addressed the need for computationally-based, automatic tools for synthesizing available data about individual consensus sequences and local compositional patterns into the composite objects (e.g., genes) that are -- as composite entities -- the true object of interest when scanning DNA sequences. The workshop was structured to promote sustained informal contact and exchange of expertise between molecular biologists, computer scientists, and mathematicians. No participant stayed for less than one week, and most attended for two or three weeks. Computers, software, and databases were available for use as electronic blackboards'' and as the basis for collaborative exploration of ideas being discussed and developed at the workshop. 23 refs., 2 tabs.

  16. Alpha-synuclein gene structure,evolution,and protein aggregation

    Lili Xiong; Peng Zhao; Zhiyun Guo; Jianhua Zhang; Diqiang Li; Canquan Mao


    α-synuclein,a member of the synuclein family,is predominately expressed in brain tissues,where it is the major component of Lewy bodies,the major hallmark of Parkinson's disease.We analyzed the phylogenetics,gene structure,and effects of different forms of α-synuclein on in vitro protein aggregation.The synuclein phylogenetic tree showed that sequences could be classified into α,β,and γ protein groups.The orthologous gene α-,β-and γ-synuclein showed similar evolutionary distance to the paralogous gene α-,β-and γ-synuclein.Bioinformatics analysis suggests that the amino-acid sequence of human α-synuclein can be divided into three regions: N-terminal amphipathic region(1-60),central hydrophobic non-amyloid beta component segment(61-95),and the C-terminal acidic part(96-140).The mutant site of A30P is at the second exon of α-synuclein,whereas E46K is located at the third exon of α-synuclein.α-synuclein alternative splicing results in four isomers,and five exons,all of which participate in protein coding,comprising 140 amino acids to produce the major α-synuclein in vivo.The threeα-synuclein isoforms are products of alternative splicing,α-synuclein 126,112 and 98.We also review the genetic and cellular factors that affect the aggregation of α-synuclein and compounds that inhibit aggregation.A better understanding of α-synuclein sequences,structure,and function may allow better targeted therapy and diagnosis of α-synuclein in Parkinson's disease and other neurodegenerative diseases.

  17. Engineering robust and tunable spatial structures with synthetic gene circuits.

    Kong, Wentao; Blanchard, Andrew E; Liao, Chen; Lu, Ting


    Controllable spatial patterning is a major goal for the engineering of biological systems. Recently, synthetic gene circuits have become promising tools to achieve the goal; however, they need to possess both functional robustness and tunability in order to facilitate future applications. Here we show that, by harnessing the dual signaling and antibiotic features of nisin, simple synthetic circuits can direct Lactococcus lactis populations to form programmed spatial band-pass structures that do not require fine-tuning and are robust against environmental and cellular context perturbations. Although robust, the patterns are highly tunable, with their band widths specified by the external nisin gradient and cellular nisin immunity. Additionally, the circuits can direct cells to consistently generate designed patterns, even when the gradient is driven by structured nisin-producing bacteria and the patterning cells are composed of multiple species. A mathematical model successfully reproduces all of the observed patterns. Furthermore, the circuits allow us to establish predictable structures of synthetic communities and controllable arrays of cellular stripes and spots in space. This study offers new synthetic biology tools to program spatial structures. It also demonstrates that a deep mining of natural functionalities of living systems is a valuable route to build circuit robustness and tunability.

  18. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R


    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  19. The specific role of pRb in p16 (INK4A) -mediated arrest of normal and malignant human breast cells.

    Bazarov, Alexey V; Lee, Won Jae; Bazarov, Irina; Bosire, Moses; Hines, William C; Stankovich, Basha; Chicas, Agustin; Lowe, Scott W; Yaswen, Paul


    RB family proteins pRb, p107 and p130 have similar structures and overlapping functions, enabling cell cycle arrest and cellular senescence. pRb, but not p107 or p130, is frequently mutated in human malignancies. In human fibroblasts acutely exposed to oncogenic ras, pRb has a specific role in suppressing DNA replication, and p107 or p130 cannot compensate for the loss of this function; however, a second p53/p21-dependent checkpoint prevents escape from growth arrest. This model of oncogene-induced senescence requires the additional loss of p53/p21 to explain selection for preferential loss of pRb function in human malignancies. We asked whether similar rules apply to the role of pRb in growth arrest of human epithelial cells, the source of most cancers. In two malignant human breast cancer cell lines, we found that individual RB family proteins were sufficient for the establishment of p16-initiated senescence, and that growth arrest in G 1 was not dependent on the presence of functional pRb or p53. However, senescence induction by endogenous p16 was delayed in primary normal human mammary epithelial cells with reduced pRb but not with reduced p107 or p130. Thus, under these circumstances, despite the presence of functional p53, p107 and p130 were unable to completely compensate for pRb in mediating senescence induction. We propose that early inactivation of pRb in pre-malignant breast cells can, by itself, extend proliferative lifespan, allowing acquisition of additional changes necessary for malignant transformation.

  20. Experimental determination and prediction of activity coefficients of RbCl in aqueous (RbCl+RbNO{sub 3}) mixture at T=298.15 K

    Zhang Jun [Chemical Engineering Department, Henan University of Science and Technology, 48 Xiyuan Road, Luoyang, Henan 471003 (China)]. E-mail:; Huang Xingyuan [Chemical Engineering Department, Henan University of Science and Technology, 48 Xiyuan Road, Luoyang, Henan 471003 (China); Xia Shuping [Institute of Salt Lakes, Chinese Academy of Sciences, Xi' an 710043 (China)


    Activity coefficients for rubidium chloride in the (RbCl+RbNO{sub 3}+H{sub 2}O) ternary system were determined from electromotive force (emf) measurements of the cell:Rb-ionselectiveelectrode(ISE) vertical bar RbCl(m{sub A}),RbNO{sub 3}(m{sub B}),H{sub 2}O vertical bar Ag vertical bar AgClat T=298.15 K and over total ionic strengths from (0.01 upto 3.50){sup -1}. The Rb{sup +} ion selective electrode (Rb-ISE) and Ag vertical bar AgCl electrode used in this work were made in our laboratory and had reasonably good Nernst responses, which demonstrate that the emf method can be applied to measure the above system with high precision. The experimental data were analyzed using the Harned rule and Pitzer model. The Harned coefficients and the Pitzer binary and ternary ionic interaction parameters for the system have been evaluated. The experimental results obey the Harned rule, and the Pitzer model can be used to describe this aqueous system satisfactorily. The activity coefficients of RbNO{sub 3}, the osmotic coefficients of the mixtures and the excess free energy of mixing were also calculated.

  1. Circular Dichroism of RbHe and RbN$_2$ Molecules

    Lancor, B; Wyllie, R; Walker, T G


    We present measurements of the circular dichroism of optically pumped Rb vapor near the D1 resonance line. Collisions with the buffer gases $^3$He and N$_2$ reduce the transparency of the vapor, even when fully polarized. We use two methods to measure this effect, show that the He results can be understood from RbHe potential curves, and show how this effect conspires with the spectral profile of the optical pumping light to increase the laser power demands for optical pumping of very optically thick samples.

  2. Booster vaccination with safe, modified, live-attenuated mutants of Brucella abortus strain RB51 vaccine confers protective immunity against virulent strains of B. abortus and Brucella canis in BALB/c mice.

    Truong, Quang Lam; Cho, Youngjae; Kim, Kiju; Park, Bo-Kyoung; Hahn, Tae-Wook


    Brucella abortus attenuated strain RB51 vaccine (RB51) is widely used in prevention of bovine brucellosis. Although vaccination with this strain has been shown to be effective in conferring protection against bovine brucellosis, RB51 has several drawbacks, including residual virulence for animals and humans. Therefore, a safe and efficacious vaccine is needed to overcome these disadvantages. In this study, we constructed several gene deletion mutants (ΔcydC, ΔcydD and ΔpurD single mutants, and ΔcydCΔcydD and ΔcydCΔpurD double mutants) of RB51 with the aim of increasing the safety of the possible use of these mutants as vaccine candidates. The RB51ΔcydC, RB51ΔcydD, RB51ΔpurD, RB51ΔcydCΔcydD and RB51ΔcydCΔpurD mutants exhibited significant attenuation of virulence when assayed in murine macrophages in vitro or in BALB/c mice. A single intraperitoneal immunization with RB51ΔcydC, RB51ΔcydD, RB51ΔcydCΔcydD or RB51ΔcydCΔpurD mutants was rapidly cleared from mice within 3 weeks, whereas the RB51ΔpurD mutant and RB51 were detectable in spleens until 4 and 7 weeks, respectively. Vaccination with a single dose of RB51 mutants induced lower protective immunity in mice than did parental RB51. However, a booster dose of these mutants provided significant levels of protection in mice against challenge with either the virulent homologous B. abortus strain 2308 or the heterologous Brucella canis strain 26. In addition, these mutants were found to induce a mixed but T-helper-1-biased humoral and cellular immune response in immunized mice. These data suggest that immunization with a booster dose of attenuated RB51 mutants provides an attractive strategy to protect against either bovine or canine brucellosis.


    缪林; 赵志泉; 季国忠; 范志宁; 金宁; 刘政; 张平; 程铁华


    Objective: To investigate the expression of p16, cyclin D1 and Rb protein in gastric carcinoma and premalignant lesions including dysplastic gastric mucosa and intestinal metaplasia gastric mucosa. Methods: Using SP immunohistochemical methods, the expression of pl6, cyclin D1 and Rb proteins was detected in 10 specimens of normal gastric mucosa, 15 specimens of dysplastic gastric mucosa, 15 specimens of intestinal metaplasia gastric mucosa, 30 specimens of gastric carcinoma. The clinical characteristics of the 30 patients with gastric carcinoma were analysed to explore the relationship between the parameter detected and biological action of gastric cancer. Results: Expression of p16 protein was detected in 90% of normal gastric mucosa, 86.67% of dysplastic gastric mucosa, 86.67% of intestinal metaplasia gastric mucosa, 36.67% of gastric carcinoma. The positive rate of p16 protein expression in gastric carcinoma is significantly lower than that in normal gastric mucosa and gastric premalignant lesions mucosa (P<0.01). Expression of cyclin D1 protein was detected in 10% of normal gastric mucosa, 20% of dysplastic gastric mucosa, 20% of intestinal metaplasia gastric mucosa, 53.33% of gastric carcinoma. The positive rate of cyclin D1, protein expression in gastric carcinoma is significantly higher than that in normal gastric mucosa and gastric premalignant lesions mucosa (P<0.05). Expression of Rb protein was detected in 90% of normal gastric mucosa, 80% of dysplastic gastric mucosa, 80% of intestinal metaplasia gastric mucosa, 50% of gastric carcinoma. The positive rate of Rb protein expression in gastric carcinoma is significantly lower than that in normal gastric mucosa (P<0.05). The expression of p16, cyclin D1 gene were associated with the degree of differentiation of gastric carcinoma, lymphnodes metastasis and distant metastasis. Conclusion: p16, Cyclin D1 and Rb gene play important role in gastric carcinoma genesis. The expression of p16, cyclin D1 and Rb gene

  4. E2F-1 binding affinity for pRb is not the only determinant of the E2F-1 activity

    Fikret Sahin, Todd L. Sladek


    Full Text Available E2F-1 is the major cellular target of pRB and is regulated by pRB during cell proliferation. Interaction between pRB and E2F-1 is dependent on the phosphorylation status of pRB. Despite the fact that E2F-1 and pRB have antagonistic activities when they are overexpressed, the role of the E2F-1-pRB interaction in cell growth largely remains unknown. Ideally, it would be better to study the properties of a pRB mutant that fails to bind to E2F, but retains all other activities. To date, no pRB mutation has been characterized in sufficient detail to show that it specifically eliminates E2F binding but leaves other interactions intact. An alternative approach to this issue is to ask whether mutations that change E2F proteins binding affinity to pRB are sufficient to change cell growth in aspect of cell cycle and tumor formation. Therefore, we used the E2F-1 mutants including E2F-1/S332-7A, E2F-1/S375A, E2F-1/S403A, E2F-1/Y411A and E2F-1/L132Q that have different binding affinities for pRB to better understand the roles of the E2F-1 phosphorylation and E2F-1-pRB interaction in the cell cycle, as well as in transformation and gene expression. Data presented in this study suggests that in vivo phosphorylation at amino acids 332-337, 375 and 403 is important for the E2F-1 and pRB interaction in vivo. However, although E2F-1 mutants 332-7, 375 and 403 showed similar binding affinity to pRB, they showed different characteristics in transformation efficiency, G0 accumulation, and target gene experiments.

  5. Retinal structure and function in achromatopsia: implications for gene therapy.

    Sundaram, Venki; Wilde, Caroline; Aboshiha, Jonathan; Cowing, Jill; Han, Colin; Langlo, Christopher S; Chana, Ravinder; Davidson, Alice E; Sergouniotis, Panagiotis I; Bainbridge, James W; Ali, Robin R; Dubra, Alfredo; Rubin, Gary; Webster, Andrew R; Moore, Anthony T; Nardini, Marko; Carroll, Joseph; Michaelides, Michel


    To characterize retinal structure and function in achromatopsia (ACHM) in preparation for clinical trials of gene therapy. Cross-sectional study. Forty subjects with ACHM. All subjects underwent spectral domain optical coherence tomography (SD-OCT), microperimetry, and molecular genetic testing. Foveal structure on SD-OCT was graded into 5 distinct categories: (1) continuous inner segment ellipsoid (ISe), (2) ISe disruption, (3) ISe absence, (4) presence of a hyporeflective zone (HRZ), and (5) outer retinal atrophy including retinal pigment epithelial loss. Foveal and outer nuclear layer (ONL) thickness was measured and presence of hypoplasia determined. Photoreceptor appearance on SD-OCT imaging, foveal and ONL thickness, presence of foveal hypoplasia, retinal sensitivity and fixation stability, and association of these parameters with age and genotype. Forty subjects with a mean age of 24.9 years (range, 6-52 years) were included. Disease-causing variants were found in CNGA3 (n = 18), CNGB3 (n = 15), GNAT2 (n = 4), and PDE6C (n = 1). No variants were found in 2 individuals. In all, 22.5% of subjects had a continuous ISe layer at the fovea, 27.5% had ISe disruption, 20% had an absent ISe layer, 22.5% had an HRZ, and 7.5% had outer retinal atrophy. No significant differences in age (P = 0.77), mean retinal sensitivity (P = 0.21), or fixation stability (P = 0.34) across the 5 SD-OCT categories were evident. No correlation was found between age and foveal thickness (P = 0.84) or between age and foveal ONL thickness (P = 0.12). The lack of a clear association of disruption of retinal structure or function in ACHM with age suggests that the window of opportunity for intervention by gene therapy is wider in some individuals than previously indicated. Therefore, the potential benefit for a given subject is likely to be better predicted by specific measurement of photoreceptor structure rather than simply by age. The ability to directly assess cone photoreceptor

  6. Neutron-proton multiplets in the odd-odd nucleus 53 37 90Rb

    Czerwiński, M.; RzÄ ca-Urban, T.; Urban, W.; BÄ czyk, P.; Sieja, K.; Timár, J.; Nyakó, B. M.; Kuti, I.; Tornyi, T. G.; Atanasova, L.; Blanc, A.; Jentschel, M.; Mutti, P.; Köster, U.; Soldner, T.; de France, G.; Simpson, G. S.; Ur, C. A.


    Medium-spin excited levels in 90Rb, populated in the fission of 235U induced by neutrons, have been observed for the first time. γ radiation from fission has been measured by using the EXILL array of Ge detectors at the cold-neutron-beam facility PF1B of the Institut Laue-Langevin, Grenoble. Low-energy levels are interpreted as members of the π p3/2 -1ν (d5/2) 3 , π f5/2 -1ν (d5/2) 3 , and π g9 /2ν (d5/2) 3 multiplets with the 0- ground state due to the seniority-3 coupling in the ν d5 /2 shell. Analogous anomalous coupling within the π g9 /2ν (d5/2) 3 configuration explains the 5+, 6+, and 7+ triplet of states, observed at medium spins, similar to the triplet seen in the N =53 isotone, 88Br. Shell-model calculations reproduce well the proposed structures in Rb,9088 and support the seniority-3 coupling in N =53 isotones and its absence in N =51 isotones. The structure of the odd-odd 88Rb and 90Rb nuclei provides an argument in favor of the collectivity building up at the neutron number N =53 .

  7. Dynamic Changes in Ginsenoside Rb 2 and Rb3 Content in Solid-state Fermentation%人参须固态发酵中皂苷 Rb 2与 Rb 3的动态变化

    闫梅霞; 崔丽丽; 许世泉; 刘俊霞; 王英平


    以人参须为发酵基质进行赤芝双向固态发酵,测定发酵过程中人参皂苷Rb2和Rb3的含量,分析固态发酵对其影响。发酵作用使基质中Rb2和Rb3含量发生显著变化,但2种皂苷含量变化不同。Rb2在发酵初期和发酵后期都出现含量先升高后降低的过程,Rb3仅在发酵初期含量先升高后降低,发酵结束时基质中未检测到2种皂苷。%Bidirectional solid-state fermentation was carried out through the strains of Ganoderma lucidum in ginseng .The content of ginseno-side Rb2 and Rb3 was determined and the impact on the ginsenoside by solid -state fermentation was analyzed .The content of Rb2 and Rb3 changed significantly through the fermentation ,but the two kinds of ginsenoside content varied differently .The content of Rb2 increased in the early fermentation stage ,then decreased in the late fermentation stage ,the level of Rb3 increased then decreased only in the early fermentation stage ,the two kinds of ginsenoside content was 0 by the end of the fermentation .

  8. Permanent Electric Dipole Moment of an Rb Atom

    黄湘友; 游佩林


    We experimentally determine the conjecture that hydrogen-like atoms such as Rb and Cs may have large permanent electric dipole moments (EDMs). The saturated Rb vapour fills a cylindrical capacitor in the experiment.The influence of the vapour dielectric medium on capacitance is measured with a digital capacitance meter. Supposing that the measurement influence comes from the permanent EDMs of Rb atoms, from the experimental result we find that the EDM is large, i.e. dRb ≥ 8.6e × 10-9 cm.

  9. Quorum Sensing Activity in Pandoraea pnomenusa RB38

    Robson Ee


    Full Text Available Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa. Various biosensors confirmed its quorum sensing properties. High resolution triple quadrupole liquid chromatography–mass spectrometry analysis was subsequently used to characterize the N-acyl homoserine lactone production profile of P. pnomenusa strain RB38, which validated that this isolate produced N-octanoyl homoserine lactone as a quorum sensing molecule. This is the first report of the production of N-octanoyl homoserine lactone by P. pnomenusa strain RB38.

  10. The human thyrotropin beta-subunit gene differs in 5' structure from murine TSH-beta genes.

    Guidon, P T; Whitfield, G K; Porti, D; Kourides, I A


    The gene encoding the beta-subunit of human thyrotropin (hTSH-beta) was isolated, and its nucleotide sequence was determined. The gene is 4.3 kb in length, consists of three exons and two introns, and is present as a single copy as determined by Southern blot analysis of total genomic DNA. The protein coding portion of the gene, which includes exons 2 and 3, was isolated from a human genomic phage library, while exon 1, which encodes only 5' untranslated mRNA sequence, was isolated from a plasmid library of size-selected genomic DNA fragments. Here we describe the isolation of the 5' untranslated exon of the hTSH-beta subunit and 5'-flanking region. The structure of the hTSH-beta gene is very similar to the previously characterized TSH-beta genes from mouse and rat. The genes from all three species have two distinct promoter regions, but while both promoters are utilized by the murine TSH-beta genes, the human TSH-beta gene apparently utilizes only the proximal promoter for transcription initiation. A striking difference in hTSH-beta gene structure compared to the murine genes is that exon 1 of the human gene is 36 nucleotides. An analysis of the mouse, rat, and human exon 1 and 5'-flanking region shows a high percentage of sequence homology, with the exception of a 9-nucleotide insertion 13 bases 3' from the proximal TATA box found in the human gene but not found in the other two species. We propose that this insertion results in the additional length of human exon 1 compared to the mouse and rat genes. By isolating the promoter region of the hTSH-beta gene, we can begin to identify specific sequences involved in the regulation of hTSH gene expression.

  11. Selective Chemosensitization of Rb Mutant Cells


    3 jopaA o E +•» to o ü 2 3 O) U. Vt3*> OOCd» Vl.3» (0 O CM ll I S j 41 • A I O O) Di (0 o CM • o 00 CO Q. o o Q. Ö...Rb) protein, and inac- tivation of both is essential for viral transformation (Lane and Crawford 1979; Linzer and Levine 1979; De- Caprio et al...wild-type MEFs expressing El A dis - played an ~10-fold increase in p53 and Mdm2 levels as compared to their ARF-deficient counterparts, the abso

  12. Molecular Mechanisms of pRB Function in Differentiation Contributing to pRB Mediated Tumor Suppression


    mutations result in elimination protein-binding functions of the A/B pocket. 1. Using coimmunoprecipitation assays for detection of pRB interacting proteins My...chromatin/nuclear matrix. Another caviat is that pRB interacting proteins are presumably low-extractable nuclear proteins. Also, epitope tag might be... interacting proteins . Due to the failure to detect selective pRB complexes applying immunoprecipitation, I used a modified yeast two-hybrid assay as a backup

  13. Identification and structural analysis of a novel snoRNA gene cluster from Arabidopsis thaliana


    A Z2 snoRNA gene cluster,consisting of four antisense snoRNA genes, was identified from Arabidopsis thaliana. The sequence and structural analysis showed that the Z2 snoRNA gene cluster might be transcribed as a polycistronic precursor from an upstream promoter, and the intergenic spacers of the gene cluster encode the 'hairpin' structures similar to the processing recognition signals of yeast Saccharomyces cerevisiae polycistronic snoRNA precursor. The results also revealed that plant snoRNA gene with multiple copies is a characteristic in common, and provides a good system for further revealing the transcription and expression mechanism of plant snoRNA gene cluster.

  14. Chromosomal mapping, gene structure and characterization of the human and murine RAB27B gene

    Huxley Clare


    Full Text Available Abstract Background Rab GTPases are regulators of intracellular membrane traffic. The Rab27 subfamily consists of Rab27a and Rab27b. Rab27a has been recently implicated in Griscelli Disease, a disease combining partial albinism with severe immunodeficiency. Rab27a plays a key role in the function of lysosomal-like organelles such as melanosomes in melanocytes and lytic granules in cytotoxic T lymphocytes. Little is known about Rab27b. Results The human RAB27B gene is organised in six exons, spanning about 69 kb in the chromosome 18q21.1 region. Exon 1 is non-coding and is separated from the others by 49 kb of DNA and exon 6 contains a long 3' untranslated sequence (6.4 kb. The mouse Rab27b cDNA shows 95% identity with the human cDNA at the protein level and maps to mouse chromosome 18. The mouse mRNA was detected in stomach, large intestine, spleen and eye by RT-PCR, and in heart, brain, spleen and kidney by Northern blot. Transient over-expression of EGF-Rab27b fusion protein in cultured melanocytes revealed that Rab27b is associated with melanosomes, as observed for EGF-Rab27a. Conclusions Our results indicate that the Rab27 subfamily of Ras-like GTPases is highly conserved in mammals. There is high degree of conservation in sequence and gene structure between RAB27A and RAB27B genes. Exogenous expression of Rab27b in melanocytes results in melanosomal association as observed for Rab27a, suggesting the two Rab27 proteins are functional homologues. As with RAB27A in Griscelli Disease, RAB27B may be also associated with human disease mapping to chromosome 18.

  15. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

    Promponas Vasilis J


    Full Text Available Abstract Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating

  16. Allergen challenge of peripheral blood mononuclear cells from patients with seasonal allergic rhinitis increases IL-17RB, which regulates basophil apoptosis and degranulation.

    Wang, H; Mobini, R; Fang, Y; Barrenäs, F; Zhang, H; Xiang, Z; Benson, M


    Previously, expression profiling has been used to analyse allergen-challenged T-helper type 2 cells, nasal biopsies and nasal fluid cells from patients with seasonal allergic rhinitis (SAR). Allergen-challenged peripheral blood mononuclear cells (PBMCs) provide a human in vitro model of how antigen-presenting cells, CD4+ T cells and effector cells such as basophils interact in allergic inflammation. To identify novel genes and pathways in allergen-challenged PBMCs from patients with SAR using gene expression profiling and functional studies. PBMCs from 11 patients with SAR and 23 healthy controls were analysed with gene expression profiling. mRNA expression of IL17RB in basophils was evaluated using quantitative real-time PCR. Membrane protein expression and apoptosis of basophils were examined by flow cytometry. Degranulation of basophils was assessed by measuring beta-hexosaminidase release. Cytokine release was measured using ELISA. Gene expression microarray analysis of allergen-challenged PBMCs showed that 209 out of 44000 genes were differentially expressed in patients compared with controls. IL17RB was the gene whose expression increased most in patients (P<0.0001). FACS analysis of PBMCs showed, for the first time, that basophils express IL-17RB. Following allergen challenge, IL-17RB protein increased significantly on basophils from patients compared with controls (P<0.05). IL-3 significantly increased both mRNA and protein expressions of IL17RB. Activation of IL-17RB by its ligand, IL-25, inhibited apoptosis of basophils. Moreover, IgE-mediated degranulation was enhanced by IL-25. Increased expression of IL-17RB on allergen-challenged basophil is regulated by IL-3, inhibits apoptosis and promotes IgE-mediated degranulation of basophils.

  17. The bovine Mx1 gene: characterization of the gene structure, alternative splicing, and promoter region.

    Kojima, Takatoshi; Oshima, Kazunaga; Watanabe, Hiroko; Komatsu, Masanori


    The Mx gene encodes an antiviral protein and is induced by type 1 interferons (IFNs). In this study, a new bovine Mx gene (designated Mx1B) was isolated from the endometrial cDNA library of the early pregnant cow. Although the Mx1B cDNA contained a single open reading frame (ORF) the same as the known Mx1, the 5' untranslated region (UTR) and 5' coding region of Mx1B were rather different from the corresponding regions of Mx1. Genomic structure analysis revealed that bovine Mx1B was an alternative splicing variant of Mx1 and had transcription regulatory sequences in the upstream region. RT-PCR and its sequencing identified another Mx1 splicing variant and demonstrated that these bovine Mx1 splicing variants were ubiquitously expressed in various tissues. Furthermore, it was found that all the bovine breeds investigated had identical splice sites of Mx1 and Mx1B. It is speculated that cattle have at least two functional Mx isoforms that might provide strong natural resistance to specific viruses.

  18. MADS-box gene evolution-structure and transcription patterns

    Johansen, Bo; Pedersen, Louise B; Skipper, Martin;


    This study presents a phylogenetic analysis of 198 MADS-box genes based on 420 parsimony-informative characters. The analysis includes only MIKC genes; therefore several genes from gymnosperms and pteridophytes are excluded. The strict consensus tree identifies all major monophyletic groups known...... three classes of MADS-box genes to be transcribed in the stamens and carpels. Thus the analysis does not support the ABC model as formulated at present....

  19. The primary structures of two leghemoglobin genes from soybean

    Hyldig-Nielsen, J J; Jensen, E O; Paludan, K


    We present the complete nucleotide sequences of two leghemoglobin genes isolated from soybean DNA. Both genes contain three intervening sequences which interrupt the two coding sequences in identical positions. The 5' and 3' flanking sequences in both genes contain conserved sequences similar...

  20. The structure of an unusual leghemoglobin gene from soybean

    Wiborg, O; Hyldig-Nielsen, J J; Jensen, E O


    A clone containing an unusual leghemoglobin (Lb) gene was isolated from a soybean DNA library present in Charon 4A phage. DNA sequence analysis revealed that the isolated Lb gene has three intervening sequences (IVS-1, IVS-2 and IVS-3) located in the same positions as those found in other Lb gene...

  1. Two dimensional fluoride ion conductor RbSn {2}F {5} studied by impedance spectroscopy and {19}F, {119}Sn, and {87}Rb NMR

    Yamada, K.; Ahmad, M. M.; Ogiso, Y.; Okuda, T.; Chikami, J.; Miehe, G.; Ehrenberg, H.; Fuess, H.


    RbSn2F5 is a two-dimensional fluoride ion conductor. It undergoes a first-order phase transition to a superionic state at 368 K. The structure of the low temperature phase has been determined from the Rietveld analysis of the X-ray powder diffraction. The dynamic properties of the fluoride ions in RbSn2F5 have been studied by impedance spectroscopy and solid state NMR. The dc ionic conductivity of this sample shows an abrupt increase at the phase transition temperature. We have obtained the hopping frequency and the concentration of the charge carriers (F- ions) at different temperatures from the analysis of the conductivity spectra using Almond-West formalism. The estimated values of the charge carriers’ concentration agree well with that determined from the structure and were found to be independent of temperature. The relatively small value of the power-law exponent, n ≈ 0.55, supports the two-dimensional property of the investigated material. Furthermore, 19F NMR with simulation has suggested the diffusive motions of the fluoride ions between different sites. In contrast, 119Sn and 87Rb NMR spectra below 250 K supported the intrinsic disordered nature due to the random distribution of the fluoride ion vacancies.

  2. Novel antifungal α-hairpinin peptide from Stellaria media seeds: structure, biosynthesis, gene structure and evolution.

    Slavokhotova, Anna A; Rogozhin, Eugene A; Musolyamov, Alexander K; Andreev, Yaroslav A; Oparin, Peter B; Berkut, Antonina A; Vassilevski, Alexander A; Egorov, Tsezi A; Grishin, Eugene V; Odintsova, Tatyana I


    Plant defense against disease is a complex multistage system involving initial recognition of the invading pathogen, signal transduction and activation of specialized genes. An important role in pathogen deterrence belongs to so-called plant defense peptides, small polypeptide molecules that present antimicrobial properties. Using multidimensional liquid chromatography, we isolated a novel antifungal peptide named Sm-AMP-X (33 residues) from the common chickweed (Stellaria media) seeds. The peptide sequence shows no homology to any previously described proteins. The peculiar cysteine arrangement (C(1)X3C(2)XnC(3)X3C(4)), however, allocates Sm-AMP-X to the recently acknowledged α-hairpinin family of plant defense peptides that share the helix-loop-helix fold stabilized by two disulfide bridges C(1)-C(4) and C(2)-C(3). Sm-AMP-X exhibits high broad-spectrum activity against fungal phytopathogens. We further showed that the N- and C-terminal "tail" regions of the peptide are important for both its structure and activity. The truncated variants Sm-AMP-X1 with both disulfide bonds preserved and Sm-AMP-X2 with only the internal S-S-bond left were progressively less active against fungi and presented largely disordered structure as opposed to the predominantly helical conformation of the full-length antifungal peptide. cDNA and gene cloning revealed that Sm-AMP-X is processed from a unique multimodular precursor protein that contains as many as 12 tandem repeats of α-hairpinin-like peptides. Structure of the sm-amp-x gene and two related pseudogenes sm-amp-x-ψ1 and sm-amp-x-ψ2 allows tracing the evolutionary scenario that led to generation of such a sophisticated precursor protein. Sm-AMP-X is a new promising candidate for engineering disease resistance in plants.

  3. Na,K-ATPase characterized in artificial membranes. 2. Successive measurement of ATP-driven Rb-accumulation, ouabain-blocked Rb-flux and palytoxin-induced Rb-efflux.

    Anner, B M; Moosmayer, M


    The Na,K-ATPase is a multifunctional system anchored in the membrane of eukaryotic cells; it is responsible for the establishment and regulation of the Na/K balance of cell and organism by a stoichiometric mechanism linking Na extrusion to K uptake and ATP hydrolysis. The receptor for cardioactive steroids such as digoxin and ouabain is located at the extracellular surface of the system. Conversely, palytoxin, the most potent animal toxin, exerts its toxic effect by creating nonspecific leaks in the cell membrane leading to K-efflux and influx of Na and Ca ions. Ouabain prevents the pore-forming action of palytoxin in cells and therefore Na,K-ATPase is suspected to be the common receptor of ouabain and palytoxin. We have developed an artificial membrane system to determine structure-function relationships and ligand interactions of purified Na,K-ATPase: two-sided, bi-directional ATP-filled liposomes. In this system, ATP-driven 86Rb accumulation, arrest of 86Rb-uptake by ouabain, and palytoxin-induced 86Rb-leak were measured successively in the same preparation. Ouabain prevented the leak when the enzyme was ouabain-sensitive (rabbit kidney) but not when it was ouabain-resistant (rat kidney). On the basis of these data in conjunction with conformational analyses, allosteric conformational competition for the ouabain-palytoxin antagonism is proposed.

  4. Informational structure of genetic sequences and nature of gene splicing

    Trifonov, E. N.


    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  5. Dosage effect of high-amylose modifier gene(s) on the starch structure of maize amylose-extender mutant.

    Jiang, Hongxin; Campbell, Mark; Wu, Yusheng; Du, Shuangkui; Srichuwong, Sathaporn; Jane, Jay-Lin


    The objective of this study was to investigate how dosages of high-amylose modifier (HAM) gene(s) affected the structure of maize amylose extender (ae) mutant starch. GEMS-0067 (G), a homozygous mutant of ae and the HAM gene(s), and H99ae (H), an ae single mutant, were self-pollinated or inter-crossed to produce maize endosperms of G/G, G/H, H/G, and H/H with 3, 2, 1, and 0 doses of HAM gene(s), respectively. Endosperm starch was fractionated into amylopectin, amylose, and intermediate component (IC) of large and small molecular weights using 1-butanol precipitation of amylose followed by gel-permeation chromatography. Increases in the dosage of HAM gene(s) from 0 to 3 decreased the amylopectin content. The HAM-gene dosage significantly changed the branch chain-length of small-molecular-weight IC, but had little effect on the branch chain-length distributions of amylopectin and large-molecular-weight IC and the molecular structure of amylose.

  6. Identification and cloning of the cDNA of a Rb-associated protein RAP140a

    李权; 闻宏; 敖世洲


    Rb exerts important physiological functions in cell-cycle control, gene expression, cell differentiation, apoptosis, development and tumorigenesis by interacting with many cellular proteins. Using human partial Rb as bait, we screened a human fetal brain cDNA library through yeast two-hybrid system and obtained six novel cDNA fragments. Among them, one cDNA fragment corresponds to two different transcripts, 7 kb and 9 kb in Northern blot analysis. These two transcripts showed uniform distribution in various human tissues. We cloned the full-length cDNA of a 7.2 kb transcript through three times PCR amplifications. It was named RAP140a and predicted to encode a 1 233 amino acids hydrophilic protein. RAP140a was mapped to chromosome 3p13-p14.1. RAP140a may be functionally related to the intracellular translocation of Rb or other proteins.

  7. Identification and cloning of the cDNA of a Rb-associated protein RAP140a


    Rb exerts important physiological functions in cell-cycle control, gene expression, cell differentiation, apoptosis, development and tumorigenesis by interacting with many cellular proteins. Using human partial Rb as bait, we screened a human fetal brain cDNA library through yeast two-hybrid system and obtained six novel cDNA fragments. Among them, one cDNA fragment corre-sponds to two different transcripts, 7 kb and 9 kb in Northern blot analysis. These two transcripts showed uniform distribution in various human tissues. We cloned the full-length cDNA of a 7.2 kb transcript through three times PCR amplifications. It was named RAP140a and predicted to encode a 1 233 amino acids hydrophilic protein. RAP140a was mapped to chromosome 3p13-p14.1. RAP140a may be functionally related to the intracellular translocation of Rb or other proteins.

  8. Precision study of the $\\beta$-decay of $^{74}$Rb

    Van Duppen, P L E; Lunney, D


    We are proposing a high-resolution study of the $\\beta$-decay of $^{74}$Rb in order to extrapolate our precision knowledge of the superallowed $\\beta$-decays from the sd and fp shells towards the medium-heavy Z=N nuclei. The primary goal is to provide new data for testing the CVC hypothesis and the unitarity condition of the CKM matrix of the Standard Model. The presented programme would involve the careful measurements of the decay properties of $^{74}$Rb including the branching ratios to the excited states as well as the precise determination of the decay energy of $^{74}$Rb. The experimental methods readily available at ISOLDE include high-transmission conversion electron spectroscopy, $\\gamma$-ray spectroscopy as well as the measurements of the masses of $^{74}$Rb and $^{74}$Kr using two complementary techniques, ISOLTRAP and MISTRAL. The experiment would rely on a high-quality $^{74}$Rb beam available at ISOLDE with adequate intensity.

  9. Analysis list: RB1 [Chip-atlas[Archive

    Full Text Available RB1 Prostate,Uterus + hg19,, ...

  10. 75 FR 51654 - Airworthiness Directives; Rolls-Royce plc (RR) RB211-22B and RB211-524 Series Turbofan Engines


    ...-10] RIN 2120-AA64 Airworthiness Directives; Rolls-Royce plc (RR) RB211-22B and RB211-524 Series.... The FAA amends Sec. 39.13 by adding the following new AD: 2010-17-10 Rolls-Royce plc: Amendment 39... AD applies to Rolls-Royce plc RB211-22B series and RB211-524B4-D-02, RB211-524D4-19,...

  11. Preparation and performance of Si coating on RB-SiC mirror for surface modification%RB-SiC表面改性Si涂层的制备与性能

    苑永涛; 刘红; 邵传兵; 陈益超; 方敬忠


    In order to manufacture reaction bonded silicon carbide(RB-SiC) mirrors of fine optical surface, 100 μm thick Si coatings were prepared by RF magnetron sputtering on RB-SiC substrates of 70 mm diameter and then polished. Tests with ZYGO surface profilometer show that the RMS surface roughness of the surface-modified RB-SiC achieves 0. 496 nm. X-ray diffraction analyses reveal the polycrystalline structure of the Si coatings. Moreover, the adhesion between Si coating and RB-SiC substrate measured by direct pull-off method is more than 10. 7 MPa. Therefore, the magnetron sputtered Si coating can satisfy the requirements of RB-SiC surface modification.%为了获得高质量光学表面的碳化硅反射镜,利用射频磁控溅射方法,在直径70 mm的RB-SiC基片上沉积了厚约100 μm的Si改性涂层,对改性层进行超光滑加工,并对改性层的表面形貌及性能进行了测试.ZYGO表面粗糙度仪测试结果表明,抛光后Si改性涂层表面粗糙度均方根值达到了0.496 nm;X射线衍射仪测试显示,制备Si改性涂层为多晶结构;使用拉力机做附着力测试,结果表明膜基附着力大于10.7 MPa.证明采用磁控溅射技术制备的Si改性涂层均匀、致密、附着力好,能够满足RB-SiC材料表面改性要求.

  12. Cooperativity of Rb, Brca1, and p53 in malignant breast cancer evolution.

    Prashant Kumar

    Full Text Available Breast cancers that are "triple-negative" for the clinical markers ESR1, PGR, and HER2 typically belong to the Basal-like molecular subtype. Defective Rb, p53, and Brca1 pathways are each associated with triple-negative and Basal-like subtypes. Our mouse genetic studies demonstrate that the combined inactivation of Rb and p53 pathways is sufficient to suppress the physiological cell death of mammary involution. Furthermore, concomitant inactivation of all three pathways in mammary epithelium has an additive effect on tumor latency and predisposes highly penetrant, metastatic adenocarcinomas. The tumors are poorly differentiated and have histologic features that are common among human Brca1-mutated tumors, including heterogeneous morphology, metaplasia, and necrosis. Gene expression analyses demonstrate that the tumors share attributes of both Basal-like and Claudin-low signatures, two molecular subtypes encompassed by the broader, triple-negative class defined by clinical markers.

  13. Anti-amnestic and anti-aging effects of ginsenoside Rg1 and Rb1 and its mechanism of action

    Yong CHENG; Li-hong SHEN; Jun-tian ZHANG


    In the present paper, we overview the discovery of new biological activities induced by ginsenoside Rg1 and Rb1 and discuss possible mechanisms of action. Both compounds could increase neural plasticity in efficacy and structure; espe cially Rg1, as one small molecular drug, can increase proliferation and differentia tion of neural progenitor cells in dentate gyms of hippocampus of normal adult mice and global ischemia model in gerbils. This finding has great value for treat ment of Alzheimer's disease and other neurodegenerative disorders which is characterized by neurons loss. Increase of expression of brain derived neurotrophic factor, Bcl-2 and antioxidant enzyme, enhanced new synapse formation, inhibition of apoptosis and calcium overload are also important neuron protective factors. Rg1 and Rb1 have common effects, but there are some differences in pharmacol ogy and mechanism. These differences may attribute to their different chemical structure. Rg1 is panaxtriol with two sugars, while Rb1 is panaxtriol with four sugars.

  14. RB1 Methylation by SMYD2 Enhances Cell Cycle Progression through an Increase of RB1 Phosphorylation

    Hyun-Soo Cho


    Full Text Available It is well known that RB functions are regulated by posttranslational modifications such as phosphorylation and acetylation, but the significance of lysine methylation on RB has not been fully elucidated. Our expression analysis of SMYD2 by quantitative real-time polymerase chain reaction showed that expression levels of SMYD2 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (P < .0001, and its expression levels in tumor tissues were much higher than those of any other normal tissues. SMYD2 knockdown resulted in the suppression of cancer cell growth, and cell cycle analysis indicated that SMYD2 might play a crucial role in the G1/S transition. According to an in vitro methyltransferase assay, we found that SMYD2 methylates RB1 protein, and liquid chromatography-tandem mass spectrometry analysis revealed lysine 810 of RB1 to be methylated by SMYD2. Importantly, this methylation enhanced Ser 807/811 phosphorylation of RB1 both in vitro and in vivo. Furthermore, we demonstrated that methylated RB1 accelerates E2F transcriptional activity and promotes cell cycle progression. SMYD2 is an important oncoprotein in various types of cancer, and SMYD2-dependent RB1 methylation at lysine 810 promotes cell cycle progression of cancer cells. Further study may explore SMYD2-dependent RB1 methylation as a potential therapeutic target in human cancer.

  15. Structure, tissue distribution, and chromosomal localization of the prepronociceptin gene.

    Mollereau, C; Simons, M J; Soularue, P; Liners, F; Vassart, G; Meunier, J C; Parmentier, M


    Nociceptin (orphanin FQ), the newly discovered natural agonist of opioid receptor-like (ORL1) receptor, is a neuropeptide that is endowed with pronociceptive activity in vivo. Nociceptin is derived from a larger precursor, prepronociceptin (PPNOC), whose human, mouse, and rat genes we have now isolated. The PPNOC gene is highly conserved in the three species and displays organizational features that are strikingly similar to those of the genes of preproenkephalin, preprodynorphin, and preproopiomelanocortin, the precursors to endogenous opioid peptides, suggesting the four genes belong to the same family-i.e., have a common evolutionary origin. The PPNOC gene encodes a single copy of nociceptin as well as of other peptides whose sequence is strictly conserved across murine and human species; hence it is likely to be neurophysiologically significant. Northern blot analysis shows that the PPNOC gene is predominantly transcribed in the central nervous system (brain and spinal cord) and, albeit weakly, in the ovary, the sole peripheral organ expressing the gene. By using a radiation hybrid cell line panel, the PPNOC gene was mapped to the short arm of human chromosome 8 (8p21), between sequence-tagged site markers WI-5833 and WI-1172, in close proximity of the locus encoding the neurofilament light chain NEFL. Analysis of yeast artificial chromosome clones belonging to the WC8.4 contig covering the 8p21 region did not allow to detect the presence of the gene on these yeast artificial chromosomes, suggesting a gap in the coverage within this contig.

  16. Observation of Quantum Beating in rb at 2.1 THz and 18.2 THz: Long-Range Rb^{*}-Rb Interactions.

    Goldshlag, William; Ricconi, Brian J.; Eden, J. Gary


    The interaction of Rb 7s ^{2}S_{1/2}, 5d ^{2}D_{3/2,5/2} and 5p ^{2}P_{3/2} atoms with the background species at long range (100-1000Å) has been observed by pump-probe ultrafast laser spectroscopy. Parametric four-wave mixing in Rb vapor with pairs of 50-70 fs pulses produces coherent Rb 6P-5S emission at 420 nm that is modulated by Rb quantum beating. The two dominant beating frequencies are 18.2 THz and 2.07 THz, corresponding to quantum beating between 7S and 5D states and to the (5D-5P_{3/2})-(5P_{3/2}-5S) defect, respectively. Analysis of Rabi oscillations in these pump-probe experiments allows for the mean interaction energy at long range to be determined. The figure shows Fourier transform spectra of representative Rabi oscillation waveforms. The waveform and spectrum at left illustrate quantum beating in Rb at 2.1 THz. The spectrum at right is dominated by the 18.2 THz frequency component generated by 7S-5D beating in Rb. Insets show respective temporal behaviors of the 6P-5S line near the coherent transient (zero interpulse delay).

  17. A cold 87Rb atomic beam

    Wang Xiao-Jia; Feng Yan-Ying; Xue Hong-Bo; Zhou Zhao-Ying; Zhang Wen-Dong


    We demonstrate an experimental setup for the production of a beam source of cold 87Rb atoms.The atoms are extracted from a trapped cold atomic cloud in an unbalanced three-dimensional magneto-optical trap.Via a radiation pressure difference generated by a specially designed leak tunnel along one trapping laser beam,the atoms are pushed out continuously with low velocities and a high flux.The most-probable velocity in the beam is varied from 9 m/s to 19 m/s by varying the detuning of the trapping laser beams in the magneto-optical trap and the flux can be tuned up to 4× 109 s-1 by increasing the intensity of the trapping beams.We also present a simple model for describing the dependence of the beam performance on the magneto-optical trap trapping laser intensity and the detuning.

  18. Angular-momentum couplings in long-range Rb$_2$ Rydberg molecules

    Anderson, David A; Raithel, Georg


    We study angular-momentum couplings in $^{87}$Rb$_2$ Rydberg molecules formed between Rydberg and 5S$_{1/2}$ ground-state atoms. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering of the Rydberg electron with the 5S$_{1/2}$ atom, along with the fine structure coupling of the Rydberg atom and hyperfine structure coupling of the 5S$_{1/2}$ atom. We discuss the effects of these couplings on the adiabatic molecular potentials. We obtain bound-state energies, lifetimes, and electric and magnetic dipole moments for the vibrational ground states of the $^{87}$Rb$(n$D$+5$S$_{1/2})$ molecules in all adiabatic potentials, with fine and hyperfine structure included. We also study the effect of the hyperfine structure on the deep $^3$S-wave- and $^3$P-wave-dominated adiabatic molecular potentials, which support high-$\\ell$ $^{87}$Rb$_2$ Rydberg molecules.

  19. Effect of Guest Atom Composition on the Structural and Vibrational Properties of the Type II Clathrate-Based Materials AxSi136, AxGe136 and AxSn136 (A = Na, K, Rb, Cs; 0 ≤ x ≤ 24

    Dong Xue


    Full Text Available Type II clathrates are interesting due to their potential thermoelectric applications. Powdered X-ray diffraction (XRD data and density functional calculations for NaxSi136 found a lattice contraction as x increases for 0 < x < 8 and an expansion as x increases for x > 8. This is explained by XRD data that shows that as x increases, the Si28 cages are filled first for x < 8 and the Si20 cages are then filled for x > 8. Motivated by this work, here we report the results of first-principles calculations of the structural and vibrational properties of the Type II clathrate compounds AxSi136, AxGe136, and AxSn136. We present results for the variation of the lattice constants, bulk moduli, and other structural parameters with x. These are contrasted for the Si, Ge, and Sn compounds and for guests A = Na, K, Rb, and Cs. We also present calculated results of phonon dispersion relations for Na4Si136, Na4Ge136, and Na4Sn136 and we compare these for the three materials. Finally, we present calculated results for the elastic constants in NaxSi136, NaxGe136, and NaxSn136 for x = 4 and 8. These are compared for the three hosts, as well as for the two compositions.

  20. Genome-wide identification of structural variants in genes encoding drug targets

    Rasmussen, Henrik Berg; Dahmcke, Christina Mackeprang


    The objective of the present study was to identify structural variants of drug target-encoding genes on a genome-wide scale. We also aimed at identifying drugs that are potentially amenable for individualization of treatments based on knowledge about structural variation in the genes encoding the...

  1. The cooperative effect of p53 and Rb in local nanotherapy in a rabbit VX2 model of hepatocellular carcinoma

    Dong S


    Full Text Available Shengli Dong,1 Qibin Tang,2 Miaoyun Long,3 Jian Guan,4 Lu Ye,5 Gaopeng Li6 1Department of General Surgery, The Second Hospital of Shanxi Medical University, Shanxi Medical University, Taiyuan, Shanxi Province, 2Department of Hepatobiliopancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 3Department of Thyroid and Vascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 4Department of Radiology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 5Infection Department, Guangzhou No 8 Hospital, Guangzhou, Guangdong Province, 6Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, People's Republic of China Background/aim: A local nanotherapy (LNT combining the therapeutic efficacy of trans-arterial embolization, nanoparticles, and p53 gene therapy has been previously presented. The study presented here aimed to further improve the incomplete tumor eradication and limited survival enhancement and to elucidate the molecular mechanism of the LNT. Methods: In a tumor-targeting manner, recombinant expressing plasmids harboring wild-type p53 and Rb were either co-transferred or transferred separately to rabbit hepatic VX2 tumors in a poly-L-lysine-modified hydroxyapatite nanoparticle nanoplex and Lipiodol® (Guerbet, Villepinte, France emulsion via the hepatic artery. Subsequent co-expression of p53 and Rb proteins within the treated tumors was investigated by Western blotting and in situ analysis by laser-scanning confocal microscopy. The therapeutic effect was evaluated by the tumor growth velocity, apoptosis and necrosis rates, their sensitivity to Adriamycin® (ADM, mitomycin C, and fluorouracil, the microvessel density of tumor tissue, and the survival time of animals. Eventually, real-time polymerase chain reaction and enhanced chemiluminescence Western blotting

  2. Rovibrational dynamics of the RbCs molecule in static electric fields. Classical study

    Arnaiz, Pedro F.; Iñarrea, Manuel [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain); Salas, J. Pablo, E-mail: [Área de Física, Universidad de la Rioja, E-26006 Logroño (Spain)


    We study the classical dynamics of the RbCs molecule in the presence of a static electric field. Under the Born–Oppenheimer approximation, we perform a rovibrational investigation which includes the interaction of the field with the molecular polarizability. The stability of the equilibrium points and the phase space structure of the system are explored in detail. We find that, for strong electric fields or for energies close to the dissociation threshold, the molecular polarizability causes relevant effects on the system dynamics. -- Highlights: ► We study the classical rovibrational dynamics of the alkali polar dimer RbCs. ► In the model we consider the interaction of the field with the molecular polarizability. ► The potential energy surface is studied depending on the electric field strength. ► Using surfaces of section we study the phase space structure. ► We find that the molecular polarizability causes relevant effects on the system dynamics.

  3. TGFbeta-mediated formation of pRb-E2F complexes in human myeloid leukemia cells.

    Hu, Xiao Tang


    TGFbeta is well known for its inhibitory effect on cell cycle G1 checkpoint kinases. However, its role in the control of pRb-E2F complexes is not well established. TGFbeta inhibits phosphorylation of pRb at several serine and threonine residues and regulates the association of E2F transcription factors with pRb family proteins. Recent studies found that predominantly E2F-4, p130, and histone deacetylase (HDAC) are found to bind to corresponding E2F-responsive promoters in G0/G1 phase. As cells progress through mid-G1, p130-E2F4 complex are replaced by p107-E2F4 followed by activators E2F1, 2, and 3. pRb was not detectable in the promoters containing the E2F-responsive site in cycling cells but was associated with E2F4-p130 complexes or E2F4-p107 complexes during G0/G1 phase. In human myeloid leukemia cell line, MV4-11, TGFbeta upregulated pRb-E2F-4 and p130-E2F-4, and downregulated p107-E2F-4 complexes. However, pRB-E2F1 and pRb-E2F3 complexes were found in proliferating cells but not in TGFbeta arrested G1 cells. In addition, electrophoretic gel mobility shift assay (EMSA) could not detect pRb-E2F DNA-binding activities either in S or G1 phase but exhibited the existence of p107-E2F4 in proliferating cells and p130-E2F4 complexes in TGFbeta-arrested G1 cells, respectively. Our data suggest that p107 and p130, but not pRb, and the repressor E2F, but not activator E2Fs, play a critical role in regulating E2F-responsive gene expression in TGFbeta-mediated cell cycle control in human myeloid leukemia cells.

  4. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

    Mørk, Søren; Holmes, Ian


    , a probabilistic dialect of Prolog. Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length......Motivation: Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM...... modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our...

  5. Optical pumping in a microfabricated Rb vapor cell using a microfabricated Rb discharge light source

    Venkatraman, V.; Kang, S.; Affolderbach, C.; Mileti, G., E-mail: [Laboratoire Temps-Fréquence, University of Neuchâtel, Neuchâtel 2000 (Switzerland); Shea, H. [Microsystems for Space Technologies Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel 2002 (Switzerland)


    Miniature (Rb discharge lamp light source, as well as (2) a conventional glass-blown Rb discharge lamp. The microfabricated Rb lamp cell is a dielectric barrier discharge (DBD) light source, having the same inner cell volume of around 40 mm{sup 3} as that of the resonance cell, both filled with suitable buffer gases. A miniature (∼2 cm{sup 3} volume) test setup based on the M{sub z} magnetometer interrogation technique was used for observation of optical-radiofrequency double-resonance signals, proving the suitability of the microfabricated discharge lamp to introduce efficient optical pumping. The pumping ability of this light source was found to be comparable to or even better than that of a conventional glass-blown lamp. The reported results indicate that the micro-fabricated DBD discharge lamp has a high potential for the development of a new class of miniature atomic clocks, magnetometers, and quantum sensors.

  6. Structure of the omega-gliadin gene family

    The '-gliadins are one of the classes of wheat seed storage proteins, but are the least characterized. In this report, an analysis is made of all available '-gliadin DNA sequences including '-gliadins genes within a large genomic clone, previously reported gene sequences, and ESTs identified from th...

  7. The genomic structure of the DMBT1 gene

    Mollenhauer, J; Holmskov, U; Wiemann, S


    Increasing evidence has accumulated for an involvement of the inactivation of tumour suppressor genes at chromosome 10q in the carcinogenesis of brain tumours, melanomas, and carcinomas of the lung, the prostate, the pancreas, and the endometrium. The gene DMBT1 (Deleted in Malignant Brain Tumour...

  8. Structure and expression of a rice hsp70 gene

    王群; 方荣祥


    A genomic hsp70 gene was isolated from a rice IR36 genomic library and 4 794 bp of the gene have been sequenoed. The 5’ flanking region of the gene contained a putative TATA box and a typical heat shock element sequence 5’-CTcgGAAccTTCgAG-3’. The amino acid sequence of the rice HSP70 deduced from the coding region shared 84%-92% homologies with those of HSP70s from other plant species. An intron 1939bp long was identified in the coding region at the codon specifying amino acid 72 (Asp), the similar position introns occurring in other intron-containing hsp70 genes. In addition, another intron of 57 bp was found in the 3’-untranslated region in the rice hsp70 gene. Southern blot hybridization showed that rice hsp70 gene family contained at least three members. Analysis of the RNA leveis with the gene-specific and non-specific probes revealed that the rice hsp70 gene expressed at normal temperature and the expression was enhanced by heat shock treatment.

  9. Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L..

    Zhi Zou

    Full Text Available WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III. Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae, comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants.

  10. Gene structure, phylogeny and expression profile of the sucrose synthase gene family in cacao (Theobroma cacao L.)

    Fupeng Li; Chaoyun Hao; Lin Yan; Baoduo Wu; Xiaowei Qin; Jianxiong Lai; Yinghui Song


    In higher plants, sucrose synthase (Sus, EC is widely considered as a key enzyme involved in sucrose metabolism. Although, several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, to date detailed information about the Sus genes is lacking for cacao. This study reports the identification of six novel Sus genes from economically important cacao tree. Analyses of the gene structure and phylogeny of the Sus genes demonstrated evolutionary conservation in the Sus family across cacao and other plant species. The expression of cacao Sus genes was investigated via real-time PCR in various tissues, different developmental phases of leaf, flower bud and pod. The Sus genes exhibited distinct but partially redundant expression profiles in cacao, with TcSus1, TcSus5 and TcSus6, being the predominant genes in the bark with phloem, TcSus2 predominantly expressing in the seed during the stereotype stage. TcSus3 and TcSus4 were significantly detected more in the pod husk and seed coat along the pod development, and showed development dependent expression profiles in the cacao pod. These results provide new insights into the evolution, and basic information that will assist in elucidating the functions of cacao Sus gene family.

  11. Gene structure, phylogeny and expression profile of the sucrose synthase gene family in cacao (Theobroma cacao L.).

    Li, Fupeng; Hao, Chaoyun; Yan, Lin; Wu, Baoduo; Qin, Xiaowei; Lai, Jianxiong; Song, Yinghui


    In higher plants, sucrose synthase (Sus, EC is widely considered as a key enzyme involved in sucrose metabolism. Although, several paralogous genes encoding different isozymes of Sus have been identified and characterized in multiple plant genomes, to date detailed information about the Sus genes is lacking for cacao. This study reports the identification of six novel Sus genes from economically important cacao tree. Analyses of the gene structure and phylogeny of the Sus genes demonstrated evolutionary conservation in the Sus family across cacao and other plant species. The expression of cacao Sus genes was investigated via real-time PCR in various tissues, different developmental phases of leaf, flower bud and pod. The Sus genes exhibited distinct but partially redundant expression profiles in cacao, with TcSus1, TcSus5 and TcSus6, being the predominant genes in the bark with phloem, TcSus2 predominantly expressing in the seed during the stereotype stage. TcSus3 and TcSus4 were significantly detected more in the pod husk and seed coat along the pod development, and showed development dependent expression profiles in the cacao pod. These results provide new insights into the evolution, and basic information that will assist in elucidating the functions of cacao Sus gene family.

  12. Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.).

    Zou, Zhi; Yang, Lifu; Wang, Danhua; Huang, Qixing; Mo, Yeyong; Xie, Guishui


    WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants.

  13. dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development.

    Ceol, C J; Horvitz, H R


    The synthetic multivulva (synMuv) genes define two functionally redundant pathways that antagonize RTK/Ras signaling during Caenorhabditis elegans vulval induction. The synMuv gene lin-35 encodes a protein similar to the mammalian tumor suppressor pRB and has been proposed to act as a transcriptional repressor. Studies using mammalian cells have shown that pRB can prevent cell cycle progression by inhibiting DP/E2F-mediated transcriptional activation. We identified C. elegans genes that encode proteins similar to DP or E2F. Loss-of-function mutations in two of these genes, dpl-1 DP and efl-1 E2F, caused the same vulval abnormalities as do lin-35 Rb loss-of-function mutations. We propose that rather than being inhibited by lin-35 Rb, dpl-1 DP and efl-1 E2F act with lin-35 Rb in transcriptional repression to antagonize RTK/Ras signaling during vulval development.

  14. Structure of the human 4-hydroxyphenylpyruvic acid dioxygenase gene (HPD)

    Awata, H.; Endo, F.; Matsuda, I. [Kumamoto Univ. (Japan)


    4-Hydroxyphenylpyruvic acid dioxygenase (HPD) is an important enzyme in tyrosine catabolism in most organisms. The activity of this enzyme is expressed mainly in the liver and developmentally regulated in mammals, and a genetic deficiency in this enzyme in humans and mice leads to hereditary tyrosinemia type 3. Using human HPD cDNA as a probe, a chromosomal gene related to HPD was isolated from human gene libraries. The human HPD gene is over 30 kb long and is split into 14 exons. The extract sizes and boundaries of exon blocks were determined, and all of the splice donor and acceptor sites conformed to the GT/AG rule. Analysis of the 5{prime} flanking sequence of the gene suggests that expression of the gene is regulated by hepatocyte-specific and liver-enriched transcription factors, as well as by hormones. These features of the 5{prime} flanking region of the gene are similar to those of other genes that are specifically expressed in hepatocytes and that are developmentally regulated. 41 refs., 2 figs., 1 tab.

  15. Structure and function of Rac genes in higher plants

    LUO Min; WU Naihu


    As the sole ubiquitous signal GTP-binding protein in higher plants, Rac genes act as pivotal molecular switches and participate in regulations of many life activities, such as cell morphogenesis and polarity growth, programmed cell death, production of H2O2, cell differentiation, and hormone reaction. Based on our work on rice Rac genes, this paper summarizes the researches on Rac genes in higher plant of the last ten years. It will help us to understand the relation between the signal tranduction and the biological functions of plant Rac.

  16. Predicting Gene Structures from Multiple RT-PCR Tests

    Kováč, Jakub; Vinař, Tomáš; Brejová, Broňa

    It has been demonstrated that the use of additional information such as ESTs and protein homology can significantly improve accuracy of gene prediction. However, many sources of external information are still being omitted from consideration. Here, we investigate the use of product lengths from RT-PCR experiments in gene finding. We present hardness results and practical algorithms for several variants of the problem and apply our methods to a real RT-PCR data set in the Drosophila genome. We conclude that the use of RT-PCR data can improve the sensitivity of gene prediction and locate novel splicing variants.

  17. Ginsenoside Rb1 directly scavenges hydroxyl radical and hypochlorous acid.

    Lü, Jian-Ming; Weakley, Sarah M; Yang, Zhen; Hu, Ming; Yao, Qizhi; Chen, Changyi


    Reactive oxygen species (ROS) have been implicated in a variety of inflammatory diseases including cardiovascular disease (CVD), cancer, diabetes, Alzheimer's disease, autism, cataracts and aging. When endogenous mechanisms for the maintenance of redox homeostasis are overwhelmed, dietary intake of antioxidants contributes substantially to balancing the body's oxidant/antioxidant status. Ginsenosides are thought to be primarily responsible for the pharmacological effect of P. ginseng root extracts on oxidative stress and inflammation. However, little is known about the underlying antioxidant mechanisms of individual ginsenoside; specifically, the reactivity of ginsenoside Rb1 with ROS has not been well studied. We found that Rb1 can significantly and selectively reduce hydroxyl radical (●OH) and hypochlorous acid (HOCl), two of the strongest ROS, with unique molecular mechanisms in a cell-free system. Rb1 directly scavenges the ●OH and protects plasmid DNA from damage induced by ●OH. ●OH likely attacks the double bond on the side chain of Rb1 as well as hydrogen atoms adjacent to the -OH groups, including those of sugar moieties. Rb1 also shows a high reactivity to HOCl and effectively inhibits HOCl-induced tyrosine chlorination in a cell free system. HOCl is added to the double bond of Rb1; the -Cl group and -OH group of HOCl possibly bond at C-24 and C-25 of Rb1 based on the regioselectivity of Markovnikov's Rule. To our knowledge, this is the first demonstration that ginsenoside Rb1 scavenges HOCl and protects tyrosine from HOCl-induced chlorination. Thus, this study reveals unique antioxidant mechanisms of individual ginsenoside Rb1, which may contribute to the pharmacological effect of P. ginseng and to the development of effective strategies for clinical applications of ginsenosides.

  18. Topologically identical, but geometrically isomeric layers in hydrous α-, β-Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O and anhydrous Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})

    Yu, Na; Klepov, Vladislav V. [Forschungszentrum Jülich GmbH, Institute for Energy and Climate Research (IEK-6), 52428 Jülich (Germany); Villa, Eric M. [Department of Chemistry, Creighton University, 2500 California Plaza, Omaha NE 68178 (United States); Bosbach, Dirk [Forschungszentrum Jülich GmbH, Institute for Energy and Climate Research (IEK-6), 52428 Jülich (Germany); Suleimanov, Evgeny V. [Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, 603950 Nizhny Novgorod (Russian Federation); Depmeier, Wulf [Institut für Geowissenschaften, Universität zu Kiel, 24118 Kiel (Germany); Albrecht-Schmitt, Thomas E., E-mail: [Department of Chemistry and Biochemistry, Florida State University, 102 Varsity Way, Tallahassee, FL 32306-4390 (United States); Alekseev, Evgeny V., E-mail: [Forschungszentrum Jülich GmbH, Institute for Energy and Climate Research (IEK-6), 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)


    The hydrothermal reaction of uranyl nitrate with rubidium nitrate and arsenic (III) oxide results in the formation of polymorphic α- and β-Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O (α-, β-RbUAs) and the anhydrous phase Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})] (RbUAs). These phases were structurally, chemically and spectroscopically characterized. The structures of all three compounds are based upon topologically identical, but geometrically isomeric layers. The layers are linked with each other by means of the Rb cations and hydrogen bonding. Dehydration experiments demonstrate that water deintercalation from hydrous α- and β-RbUAs yields anhydrous RbUAs via topotactic reactions. - Graphical abstract: Three different layer geometries observed in the structures of Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})] and α- and β- Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O. Two different coordination environments of uranium polyhedra (types I and II) are shown schematically on the top of the figure. - Highlights: • Three new uranyl arsenates were synthesized from the hydrothermal reactions. • The phases consist of the topologically identical but geometrically different layers. • Topotactic transitions were observed in the processes of mono-hyrates dehydration.

  19. Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12.

    Deeley, M C; Yanofsky, C


    The tryptophanase structural gene, tnaA, of Escherichia coli K-12 was cloned and sequenced. The size, amino acid composition, and sequence of the protein predicted from the nucleotide sequence agree with protein structure data previously acquired by others for the tryptophanase of E. coli B. Physiological data indicated that the region controlling expression of tnaA was present in the cloned segment. Sequence data suggested that a second structural gene of unknown function was located distal ...

  20. Structure of the gene encoding columbid annexin Icp35.

    Hitti, Y S; Horseman, N D


    The cp35 gene, encoding an annexin I (AnxI) cropsac 35-kDa protein (cp35) from the pigeon, consists of 13 exons and twelve introns. The borders of exons 2-13 were mapped by comparison with the known cDNA sequence. A 5-kb sequence containing exons 1, 2, and 3, and 1.4 kb of 5'-flanking DNA, is presented. The transcription start point was mapped by S1 nuclease protection. The region of the cp35 mRNA sequence, which we had previously shown to be profoundly different from mammalian anxI, is located in the first half of exon 3. Whereas human anxI is known to be single copy, Southern analysis of pigeon genomic DNA and genomic clones demonstrated multiple anxI genes in the pigeon, diverging significantly in their 5'-termini. Pigeon vimentin, on the other hand, is encoded by a single-copy gene as it is in other birds and mammals. These experiments have demonstrated that the cp35 mRNA is transcribed from its individual gene and is not a product of alternative processing of the pigeon homolog of mammalian anxI. We speculate that the diversification of anxI genes in Columbid birds allowed the recruitment of one of these genes (cp35) for unique regulation by prolactin in the absence of post-translational regulation via residues encoded by exons 2 and 3.

  1. Gene structure and chromosomal localization of plasma kallikrein

    Beaubien, G.; Mbikay, M.; Chretien, M.; Seidah, N.G. (Clinical Research Institute of Montreal, Quebec (Canada)); Rosinski-Chupin, I. (Inst. Pasteur, Paris (France)); Mattei, M.G. (Groupe hospitalier de a Timone, Marseille (France))


    Plasma kallikrein (Fletcher factor) is a hepatic serine proteinase that participates in the early phase of blood coagulation. From two genomic libraries, the authors succeeded to isolate four overlapping clones representing the entire rat plasma kallikrein gene. Using selective DNA sequencing, polymerase chain reactions, and restriction mapping, the authors demonstrated that the gene for rat plasma kallikrein was 22 kb in length. Similar to human factor XI the authors also found that the plasma kallikrein gene is composed of 15 exons and 14 introns. A potential transcription initiation step was determined by a novel application of the polymerase chain reaction technique. Computer analysis of the 5{prime}-promoter region of this gene revealed some putative control elements that might regulate the rat plasma kallikrein gene expression. These data and the results of chromosomal localization reported in the present study for mouse (chromosome 8) and human (chromosome 4) plasma kallikrein genes strongly corroborate a genic duplication event from a common ancestor to both plasma kallikrein and factor XI.

  2. Structure and expression of the chicken calmodulin I gene

    Ye, Q; Berchtold, M W


    The chicken calmodulin I (CaMI) gene has been isolated and characterized on the level of cDNA and genomic DNA. The deduced amino acid (aa) sequence is identical to the one of chicken CaMII which consists of 148 aa. The CaMI gene contains six exons. Its intron/exon organization is identical...... to that of the chicken CaMII and the CaMI and CaMIII genes of rat and human. Expression of the CaMI gene was detected in all chicken tissues examined, although at varying levels. The gene is transcribed into four mRNAs of 0.8, 1.4, 1.7 and 4.4 kb as determined by Northern blot analysis. Our results demonstrate...... that the "multigene-one-protein" principle of CaM synthesis is not only applicable to mammals whose CaM is encoded by three different genes, but also to chickens....

  3. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.;


    Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from...... and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...... landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin...

  4. Orbital Hybridization of the Ferroelectric Rb2Cd2 (SO4)3: Origin of Domain Walls

    DUAN Yi-Feng; YI Lin


    @@ We perform first-principle calculations for the study of the orthorhombic Rb2Cd2 (SO4)3 structure. Electronic energy bands, total and partial densities of states are reported and analysed. It is found that oxygen atomic 2p electrons strongly hybridize with Rb/or Cd 4d and S 2p states, resulting in two-type ionic groups with weak couplings. It is shown that macroscopic domain walls originate from such weak-coupling ionic groups, arising at the cell boundaries. The asymmetric cation bonds (Rb-O and Cd-O) and the subsequent rotations of the SO4tetrahedra can lead to the driving force of the ferroelectric behaviour. The predicted pyroelectric current effects are observed experimentally in the ferroelectric phase.

  5. Regulation of retinoschisin secretion in Weri-Rb1 cells by the F-actin and microtubule cytoskeleton.

    Eiko Kitamura

    Full Text Available Retinoschisin is encoded by the gene responsible for X-linked retinoschisis (XLRS, an early onset macular degeneration that results in a splitting of the inner layers of the retina and severe loss in vision. Retinoschisin is predominantly expressed and secreted from photoreceptor cells as a homo-oligomer protein; it then associates with the surface of retinal cells and maintains the retina cellular architecture. Many missense mutations in the XLRS1 gene are known to cause intracellular retention of retinoschisin, indicating that the secretion process of the protein is a critical step for its normal function in the retina. However, the molecular mechanisms underlying retinoschisin's secretion remain to be fully elucidated. In this study, we investigated the role of the F-actin cytoskeleton in the secretion of retinoschisin by treating Weri-Rb1 cells, which are known to secrete retinoschisin, with cytochalasin D, jasplakinolide, Y-27632, and dibutyryl cGMP. Our results show that cytochalasin D and jasplakinolide inhibit retinoschisin secretion, whereas Y-27632 and dibutyryl cGMP enhance secretion causing F-actin alterations. We also demonstrate that high concentrations of taxol, which hyperpolymerizes microtubules, inhibit retinoschisin secretion. Our data suggest that retinoschisin secretion is regulated by the F-actin cytoskeleton, that cGMP or inhibition of ROCK alters F-actin structure enhancing the secretion, and that the microtubule cytoskeleton is also involved in this process.

  6. Comparative analysis of the gut microbiota in people with different levels of ginsenoside Rb1 degradation to compound K.

    Kyung-Ah Kim

    Full Text Available Panax ginseng (family Araliaceae which contains ginsenoside Rb1 as a main constituent is traditionally used as a remedy for cancer, inflammation, stress, and ageing. The ginsenoside Rb1 in orally administered ginseng is metabolized to bioactive compounds by gut microbiota before their absorptions to the blood. However, its metabolizing activities in individuals are significantly different as we previously demonstrated. Here, we selected 5 samples with fecal activity potently metabolizing ginsenoside Rb1 to compound K (FPG; metabolic activity, 0.058±0.029 pmol/min/mg and 5 samples with fecal activity non-metabolizing ginsenoside Rb1 to compound K (FNG from a pool of 100 subjects investigated in a previous study and analyzed fecal microbiota by 16S rRNA gene pyrosequencing. Taxonomy-based analysis showed that the population levels of Firmicutes and Proteobacteria in FPG were lower than in FNG, but those of Bacteroidetes and Tenericutes in FPG were higher than in FNG. At the genus level, the population levels of Clostridiales_uc_g, Oscillibacter, Ruminococcus, Holdemania, and Sutterella in FPG were significantly higher than in FNG, but that of Leuconostoc in FPG was lower than in FNG. The population levels of Bacteroides and Bifidobacterium, which potently metabolizes ginsenoside Rb1 to compound K were dramatically increased in FPG. The gut microbiota compositions of FPG and FNG were segregated on PCO2 by Principal Coordinate Analysis. Intestinal bacterial metabolism of ginseng, particularly ginsenoside Rb1, may be dependent on the composition of gut microbiota, such as Ruminococcus spp., Bacteroides spp. and Bifidobacterium spp.

  7. Retinoblastoma (Rb) regulates laminar dendritic arbor reorganization in retinal horizontal neurons

    Martins, Rodrigo [St. Jude Children' s Research Hospital; Davis, Denise [St. Jude Children' s Research Hospital; Dyer, Michael [St. Jude Children' s Research Hospital; Kerekes, Ryan A [ORNL; Zhang, Jiakun [St. Jude Children' s Research Hospital; Bayazitov, Ildar [St. Jude Children' s Research Hospital; Hiler, Daniel [St. Jude Children' s Research Hospital; Karakaya, Mahmut [ORNL; Frase, Sharon [St. Jude Children' s Research Hospital; Gleason, Shaun Scott [ORNL; Zakharenko, Stanislav S [ORNL; Johnson, Dianna [University of Tennessee Health Science Center, Memphis


    Neuronal differentiation with respect to the acquisition of synaptic competence needs to be regulated precisely during neurogenesis to ensure proper formation of circuits at the right place and time in development.This regulation is particularly important for synaptic triads among photoreceptors, horizontal cells (HCs), and bipolar cells in the retina, because HCs are among the rst cell types produced during development, and bipolar cells are among thel ast.HCs undergo a dramatic transition from vertically oriented neurites that form columnar arbors to overlapping laminar dendritic arbors with differentiation.However, how this process is regulated and coordinated with differentiation of photoreceptors and bipolar cells remains unknown. Previous studies have suggested that there tino-blastoma(Rb) tumor suppressor gene may play a role in horizontal cell differentiation and synaptogenesis. By combining genetic mosaic analysis of individual synaptictriads with neuroanatomic analyses and multiphoton live imaging of developing HCs, we found that Rb plays a cell-autonomous role in there organization of horizontal cell neurites as they differentiate. Aberrant vertical processes in Rb-de cient HCs form ectopic synapses with rods in the outer nuclear layer but lack bipolar dendrites. Although previous reports indicate that photoreceptor abnormalities can trigger formation of ectopic synapses, our studies now demonstrate that defects in a post synaptic partner contribute to the formation of ectopic photoreceptor synapses in the mammalian retina.

  8. Collisions of trapped ions with ultracold atoms in the [YbRb]$^+$ system

    Lamb, H D L; Goold, J; Wells, N; Lane, I


    We investigate the ultracold elastic scattering for the quasi-molecular ion of ytterbium and rubidium system, based on {\\it ab initio} calculations, including both asymptotic ionic channels. This structure has an important role in the design of hybrid ion-atom traps and quantum control of charge transfer processes. The dissociation energies and molecular constants for the lowest electronic states were calculated along with the long-range dispersion forces in order to estimate the scattering lengths. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom ($\\alpha_d=128.5$ atomic units) are in good agreement with experiment and previous calculations. Using phase shift analysis and the semiclassical approximation, for the Rb$^+$ channel the scattering length is $a_s \\approx +2815\\ a_{0}$. With the Yb$^+$ ion colliding with the Rb atom we have the complications of singlet/triplet and the presence of nearly-degenerate charge transfer states introducing uncertainty. For the triplet...

  9. Superconductivity and ferromagnetism in hole-doped RbEuFe4As4

    Liu, Yi; Liu, Ya-Bin; Tang, Zhang-Tu; Jiang, Hao; Wang, Zhi-Cheng; Ablimit, Abduweli; Jiao, Wen-He; Tao, Qian; Feng, Chun-Mu; Xu, Zhu-An; Cao, Guang-Han


    We discover a robust coexistence of superconductivity and ferromagnetism in an iron arsenide RbEuFe4As4 . The new material crystallizes in an intergrowth structure of RbFe2As2 and EuFe2As2 , such that the Eu sublattice turns out to be primitive instead of being body-centered in EuFe2As2 . The FeAs layers, featured by asymmetric As coordinations, are hole doped due to charge homogenization. Our combined measurements of electrical transport, magnetization, and heat capacity unambiguously and consistently indicate bulk superconductivity at 36.5 K in the FeAs layers and ferromagnetism at 15 K in the Eu sublattice. Interestingly, the Eu-spin ferromagnetic ordering belongs to a rare third-order transition, according to the Ehrenfest classification of phase transitions. We also identify an additional anomaly at ˜5 K, which is possibly associated with the interplay between superconductivity and ferromagnetism.

  10. Synthesis and Characterization of the Ternary Thiobismuthates A9Bi13S24 (A = K, Rb)

    Davaasuren, Bambar


    Ternary alkali metal thiobismuthates ABiS (A = K, Rb) were synthesized by direct combination reactions at 650 °C. The compounds crystallize in the monoclinic space group C2/m (no. 12) with cell parameters a = 30.919(1) Å, b = 4.1008(2) Å, c = 20.9072(9) Å, β = 105.826(3)° for KBiS (1) and a = 31.823(6) Å, b = 4.1177(8) Å, c = 21.086(4) Å, β = 105.62(3)° for RbBiS (2). The crystal structure of 1 contains a 3D [KBiS] polyanionic framework, whereas 2 consists of 2D [RbBiS] polyanionic slabs stacked along [201]. Both 1 and 2 are semiconductors with a band gap of 1.4 and 1.3 eV, respectively, which is supported by an electronic structure calculation. 1 melts congruently at 580 °C, while 2 melts incongruently at 575 °C. 1 and 2 are airstable and insoluble in water and organic solvents.

  11. Radioactivity Measurement of Short Life Nuclide 89Rb


    <正>The radioactivity of short life nuclide 89Rb produced by fast radiochemical separation was measured by the digital coincidence counting (DCC) system. In this experiment, there were a large quantity of impurities

  12. Photoemission studies of Mg and Rb layers on Zn(0 0 0 1)

    Suchodolskis, A. E-mail:; Karpus, V.; Kanski, J.; Ilver, L.; Goethelid, M.; Karlsson, U.O


    The electronic structure of the clean Zn(0 0 0 1) surface is studied by angle resolved photoemission. An earlier detected surface state at the surface Brillouin zone centre is confirmed and a new surface state is found at the surface Brilluoin zone boundary. The surface electronic structure of Zn is found to be similar to the that of Cd. Evaporation of thin films of Mg and Rb onto the Zn(0 0 0 1) surface quenches the emission from both surface states and reduces the intensity of the bulk related structures.

  13. The high-risk HPV16 E7 oncoprotein mediates interaction between the transcriptional coactivator CBP and the retinoblastoma protein pRb.

    Jansma, Ariane L; Martinez-Yamout, Maria A; Liao, Rong; Sun, Peiqing; Dyson, H Jane; Wright, Peter E


    The oncoprotein E7 from human papillomavirus (HPV) strains that confer high cancer risk mediates cell transformation by deregulating host cellular processes and activating viral gene expression through recruitment of cellular proteins such as the retinoblastoma protein (pRb) and the cyclic-AMP response element binding binding protein (CBP) and its paralog p300. Here we show that the intrinsically disordered N-terminal region of E7 from high-risk HPV16 binds the TAZ2 domain of CBP with greater affinity than E7 from low-risk HPV6b. HPV E7 and the tumor suppressor p53 compete for binding to TAZ2. The TAZ2 binding site in E7 overlaps the LxCxE motif that is crucial for interaction with pRb. While TAZ2 and pRb compete for binding to a monomeric E7 polypeptide, the full-length E7 dimer mediates an interaction between TAZ2 and pRb by promoting formation of a ternary complex. Cell-based assays show that expression of full-length HPV16 E7 promotes increased pRb acetylation and that this response depends both on the presence of CBP/p300 and on the ability of E7 to form a dimer. These observations suggest a model for the oncogenic effect of high-risk HPV16 E7. The disordered region of one E7 molecule in the homodimer interacts with the pocket domain of pRb, while the same region of the other E7 molecule binds the TAZ2 domain of CBP/p300. Through its ability to dimerize, E7 recruits CBP/p300 and pRb into a ternary complex, bringing the histone acetyltransferase domain of CBP/p300 into proximity to pRb and promoting acetylation, leading to disruption of cell cycle control.

  14. Alpha tubulin genes from Leishmania braziliensis: genomic organization, gene structure and insights on their expression.

    Ramírez, César A; Requena, José M; Puerta, Concepción J


    Alpha tubulin is a fundamental component of the cytoskeleton which is responsible for cell shape and is involved in cell division, ciliary and flagellar motility and intracellular transport. Alpha tubulin gene expression varies according to the morphological changes suffered by Leishmania in its life cycle. However, the objective of studying the mechanisms responsible for the differential expression has resulted to be a difficult task due to the complex genome organization of tubulin genes and to the non-conventional mechanisms of gene regulation operating in Leishmania. We started this work by analyzing the genomic organization of α-tubulin genes in the Leishmania braziliensis genome database. The genomic organization of L. braziliensis α-tubulin genes differs from that existing in the L. major and L. infantum genomes. Two loci containing α-tubulin genes were found in the chromosomes 13 and 29, even though the existence of sequence gaps does not allow knowing the exact number of genes at each locus. Southern blot assays showed that α-tubulin locus at chromosome 13 contains at least 8 gene copies, which are tandemly organized with a 2.08-kb repetition unit; the locus at chromosome 29 seems to contain a sole α-tubulin gene. In addition, it was found that L. braziliensis α-tubulin locus at chromosome 13 contains two types of α-tubulin genes differing in their 3' UTR, each one presumably containing different regulatory motifs. It was also determined that the mRNA expression levels of these genes are controlled by post-transcriptional mechanisms tightly linked to the growth temperature. Moreover, the decrease in the α-tubulin mRNA abundance observed when promastigotes were cultured at 35°C was accompanied by parasite morphology alterations, similar to that occurring during the promastigote to amastigote differentiation. Information found in the genome databases indicates that α-tubulin genes have been reorganized in a drastic manner along Leishmania

  15. The mammalian adult neurogenesis gene ontology (MANGO) provides a structural framework for published information on genes regulating adult hippocampal neurogenesis.

    Overall, Rupert W; Paszkowski-Rogacz, Maciej; Kempermann, Gerd


    Adult hippocampal neurogenesis is not a single phenotype, but consists of a number of sub-processes, each of which is under complex genetic control. Interpretation of gene expression studies using existing resources often does not lead to results that address the interrelatedness of these processes. Formal structure, such as provided by ontologies, is essential in any field for comprehensive interpretation of existing knowledge but, until now, such a structure has been lacking for adult neurogenesis. We have created a resource with three components 1. A structured ontology describing the key stages in the development of adult hippocampal neural stem cells into functional granule cell neurons. 2. A comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes) to the appropriate terms in our ontology. 3. An easy-to-use searchable interface to the resulting database made freely available online. The manuscript presents an overview of the database highlighting global trends such as the current bias towards research on early proliferative stages, and an example gene set enrichment analysis. A limitation of the resource is the current scope of the literature which, however, is growing by around 100 publications per year. With the ontology and database in place, new findings can be rapidly annotated and regular updates of the database will be made publicly available. The resource we present allows relevant interpretation of gene expression screens in terms of defined stages of postnatal neuronal development. Annotation of genes by hand from the adult neurogenesis literature ensures the data are directly applicable to the system under study. We believe this approach could also serve as an example to other fields in a 'bottom-up' community effort complementing the already successful 'top-down' approach of the Gene Ontology.

  16. The mammalian adult neurogenesis gene ontology (MANGO provides a structural framework for published information on genes regulating adult hippocampal neurogenesis.

    Rupert W Overall

    Full Text Available BACKGROUND: Adult hippocampal neurogenesis is not a single phenotype, but consists of a number of sub-processes, each of which is under complex genetic control. Interpretation of gene expression studies using existing resources often does not lead to results that address the interrelatedness of these processes. Formal structure, such as provided by ontologies, is essential in any field for comprehensive interpretation of existing knowledge but, until now, such a structure has been lacking for adult neurogenesis. METHODOLOGY/PRINCIPAL FINDINGS: We have created a resource with three components 1. A structured ontology describing the key stages in the development of adult hippocampal neural stem cells into functional granule cell neurons. 2. A comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes to the appropriate terms in our ontology. 3. An easy-to-use searchable interface to the resulting database made freely available online. The manuscript presents an overview of the database highlighting global trends such as the current bias towards research on early proliferative stages, and an example gene set enrichment analysis. A limitation of the resource is the current scope of the literature which, however, is growing by around 100 publications per year. With the ontology and database in place, new findings can be rapidly annotated and regular updates of the database will be made publicly available. CONCLUSIONS/SIGNIFICANCE: The resource we present allows relevant interpretation of gene expression screens in terms of defined stages of postnatal neuronal development. Annotation of genes by hand from the adult neurogenesis literature ensures the data are directly applicable to the system under study. We believe this approach could also serve as an example to other fields in a 'bottom-up' community effort complementing the already

  17. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

    Li, Yan; He, Jinzhi; He, Zhili; Zhou, Yuan; Yuan, Mengting; Xu, Xin; Sun, Feifei; Liu, Chengcheng; Li, Jiyao; Xie, Wenbo; Deng, Ye; Qin, Yujia; VanNostrand, Joy D; Xiao, Liying; Wu, Liyou; Zhou, Jizhong; Shi, Wenyuan; Zhou, Xuedong


    Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis. PMID:24671083

  18. Identification and structural analysis of a novel snoRNA gene cluster from Arabidopsis thaliana

    周惠; 孟清; 屈良鹄


    A 22 snoRNA gene cluster, consisting of four antisense snoRNA genes, was identified from Arabidopsis thaliana. The sequence and structural analysis showed that the 22 snoRNA gene cluster might be transcribed as a polycistronic precursor from an upstream promoter, and the in-tergenic spacers of the gene cluster encode the ’hairpin’ structures similar to the processing recognition signals of yeast Saccharomyces cerevisiae polycistronic snoRNA precursor. The results also revealed that plant snoRNA gene with multiple copies is a characteristic in common, and provides a good system for further revealing the transcription and expression mechanism of plant snoRNA gene cluster.

  19. Scattering lengths in isotopologues of the RbYb system

    Borkowski, Mateusz; Ciuryło, Roman; Julienne, Paul S; K{\\ke}dziera, Dariusz; Mentel, Łukasz; Tecmer, Paweł; Münchow, Frank; Bruni, Christian; Görlitz, Axel


    We model the binding energies of rovibrational levels of the RbYb molecule using experimental data from two-color photoassociation spectroscopy in mixtures of ultracold $^{87}$Rb with various Yb isotopes. The model uses a theoretical potential based on state-of-the-art \\emph{ab initio} potentials, further improved by least-squares fitting to the experimental data. We have fixed the number of bound states supported by the potential curve, so that the model is mass scaled, that is, it accurately describes the bound state energies for all measured isotopic combinations. Such a model enables an accurate prediction of the s-wave scattering lengths of all isotopic combinations of the RbYb system. The reduced mass range is broad enough to cover the full scattering lengths range from $-\\infty$ to $+\\infty$. For example, the $^{87}$Rb$^{174}$Yb system is characterized by a large positive scattering length of $+880(120)$~a.u., while $^{87}$Rb$^{173}$Yb has $a=-626(88)$~a.u.. On the other hand $^{87}$Rb$^{170}$Yb has a ...

  20. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M


    BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human...... genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed. RESULTS: We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human...... of 3 of the hairpin structures and 3 out of 9 high covariance structures in SK-N-AS cells. CONCLUSION: Our results demonstrate that many human noncoding, structured and conserved RNA genes remain to be discovered and that tissue specific tiling array data can be used in combination with computational...

  1. Serum amyloid-P component of the Armenian hamster: gene structure and comparison with structure and expression of the SAP gene from Syrian hamster.

    Rudnick, C M; Dowton, S B


    Serum amyloid P (SAP), a phylogenetically conserved pentraxin, is an integral component of all amyloid deposits. Regulation of expression of SAP gene expression is quite different in two related hamster species. In Syrian hamsters, the resting serum levels of SAP are determined by gender, and the direction of alteration following inflammation is divergent. In Armenian hamsters, SAP is not a prominent acute-phase reactant and there is no gender dimorphism of expression. The structure and expression of the SAP gene of the Armenian hamsters was investigated by isolation of genomic clones, nucleotide sequence analysis, and RNA studies. The gene structure of Armenian hamster SAP is similar to the genes of all other pentraxins studied. While the upstream regions of the SAP genes of Syrian and Armenian hamsters are quite similar, important differences in potential enhancer sites have been recognized by comparing the corresponding sequences of SAP genes from both species. Little alteration in hepatic levels of transcripts encoding SAP or CRP, the other pentraxin, were noted following administration of lipopolysaccharide to Armenian hamsters. This relative lack of response occurred despite a marked acute phase reaction documented for serum amyloid A mRNA levels.

  2. Immune Response of Calves Vaccinated with Brucella abortus S19 or RB51 and Revaccinated with RB51

    Dorneles, Elaine M. S.; Lima, Graciela K.; Teixeira-Carvalho, Andréa; Araújo, Márcio S. S.; Martins-Filho, Olindo A.; Sriranganathan, Nammalwar; Al Qublan, Hamzeh; Heinemann, Marcos B.; Lage, Andrey P.


    Brucella abortus S19 and RB51 strains have been successfully used to control bovine brucellosis worldwide; however, currently, most of our understanding of the protective immune response induced by vaccination comes from studies in mice. The aim of this study was to characterize and compare the immune responses induced in cattle prime-immunized with B. abortus S19 or RB51 and revaccinated with RB51. Female calves, aged 4 to 8 months, were vaccinated with either vaccine S19 (0.6–1.2 x 1011 CFU) or RB51 (1.3 x 1010 CFU) on day 0, and revaccinated with RB51 (1.3 x 1010 CFU) on day 365 of the experiment. Characterization of the immune response was performed using serum and peripheral blood mononuclear cells. Blood samples were collected on days 0, 28, 210, 365, 393 and 575 post-immunization. Results showed that S19 and RB51 vaccination induced an immune response characterized by proliferation of CD4+ and CD8+ T-cells; IFN-ɣ and IL-17A production by CD4+ T-cells; cytotoxic CD8+ T-cells; IL-6 secretion; CD4+ and CD8+ memory cells; antibodies of IgG1 class; and expression of the phenotypes of activation in T-cells. However, the immune response stimulated by S19 compared to RB51 showed higher persistency of IFN-ɣ and CD4+ memory cells, induction of CD21+ memory cells and higher secretion of IL-6. After RB51 revaccination, the immune response was chiefly characterized by increase in IFN-ɣ expression, proliferation of antigen-specific CD4+ and CD8+ T-cells, cytotoxic CD8+ T-cells and decrease of IL-6 production in both groups. Nevertheless, a different polarization of the immune response, CD4+- or CD8+-dominant, was observed after the booster with RB51 for S19 and RB51 prime-vaccinated animals, respectively. Our results indicate that after prime vaccination both vaccine strains induce a strong and complex Th1 immune response, although after RB51 revaccination the differences between immune profiles induced by prime-vaccination become accentuated. PMID:26352261

  3. Immune Response of Calves Vaccinated with Brucella abortus S19 or RB51 and Revaccinated with RB51.

    Dorneles, Elaine M S; Lima, Graciela K; Teixeira-Carvalho, Andréa; Araújo, Márcio S S; Martins-Filho, Olindo A; Sriranganathan, Nammalwar; Al Qublan, Hamzeh; Heinemann, Marcos B; Lage, Andrey P


    Brucella abortus S19 and RB51 strains have been successfully used to control bovine brucellosis worldwide; however, currently, most of our understanding of the protective immune response induced by vaccination comes from studies in mice. The aim of this study was to characterize and compare the immune responses induced in cattle prime-immunized with B. abortus S19 or RB51 and revaccinated with RB51. Female calves, aged 4 to 8 months, were vaccinated with either vaccine S19 (0.6-1.2 x 1011 CFU) or RB51 (1.3 x 1010 CFU) on day 0, and revaccinated with RB51 (1.3 x 1010 CFU) on day 365 of the experiment. Characterization of the immune response was performed using serum and peripheral blood mononuclear cells. Blood samples were collected on days 0, 28, 210, 365, 393 and 575 post-immunization. Results showed that S19 and RB51 vaccination induced an immune response characterized by proliferation of CD4+ and CD8+ T-cells; IFN-ɣ and IL-17A production by CD4+ T-cells; cytotoxic CD8+ T-cells; IL-6 secretion; CD4+ and CD8+ memory cells; antibodies of IgG1 class; and expression of the phenotypes of activation in T-cells. However, the immune response stimulated by S19 compared to RB51 showed higher persistency of IFN-ɣ and CD4+ memory cells, induction of CD21+ memory cells and higher secretion of IL-6. After RB51 revaccination, the immune response was chiefly characterized by increase in IFN-ɣ expression, proliferation of antigen-specific CD4+ and CD8+ T-cells, cytotoxic CD8+ T-cells and decrease of IL-6 production in both groups. Nevertheless, a different polarization of the immune response, CD4+- or CD8+-dominant, was observed after the booster with RB51 for S19 and RB51 prime-vaccinated animals, respectively. Our results indicate that after prime vaccination both vaccine strains induce a strong and complex Th1 immune response, although after RB51 revaccination the differences between immune profiles induced by prime-vaccination become accentuated.

  4. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.


    and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...


    We have sequenced the structural gene and flanking regions for lanosterol 14 alpha-demethylase (14DM) from Saccharomyces cerevisiae. An open reading frame of 530 codons encodes a 60.7-kDa protein. When this gene is disrupted by integrative transformation, the resulting strain req...

  6. Genomic structure of the human BCCIP gene and its expression in cancer.

    Meng, Xiangbing; Liu, Jingmei; Shen, Zhiyuan


    Human BCCIPalpha (Tok-1alpha) is a BRCA2 and CDKN1A (Cip1, p21) interacting protein. Our previous studies have showed that overexpression of BCCIPalpha inhibits the growth of certain tumor cells [Oncogene 20 (2001) 336]. In this study, we report the genomic structure of the human BCCIP gene, which contains nine exons. Alternative splicing of the 3'-terminal exons produces two isoforms of BCCIP transcripts, BCCIPalpha and BCCIPbeta. The BCCIP gene is flanked by two genes that are transcribed in the opposite orientation of the BCCIP gene. It lies head-to-head and shares a bi-directional promoter with the uroporphyrinogen III synthase (UROS) gene. The last three exons of BCCIP gene overlap the 3'-terminal seven exons of a DEAD/H helicase-like gene (DDX32). Using a matched normal/tumor cDNA array, we identified a reduced expression of BCCIP in kidney tumor, suggesting a role of BCCIP in cancer etiology.

  7. Gene Structures, Classification, and Expression Models of the DREB Transcription Factor Subfamily in Populus trichocarpa

    Yunlin Chen


    Full Text Available We identified 75 dehydration-responsive element-binding (DREB protein genes in Populus trichocarpa. We analyzed gene structures, phylogenies, domain duplications, genome localizations, and expression profiles. The phylogenic construction suggests that the PtrDREB gene subfamily can be classified broadly into six subtypes (DREB A-1 to A-6 in Populus. The chromosomal localizations of the PtrDREB genes indicated 18 segmental duplication events involving 36 genes and six redundant PtrDREB genes were involved in tandem duplication events. There were fewer introns in the PtrDREB subfamily. The motif composition of PtrDREB was highly conserved in the same subtype. We investigated expression profiles of this gene subfamily from different tissues and/or developmental stages. Sixteen genes present in the digital expression analysis had high levels of transcript accumulation. The microarray results suggest that 18 genes were upregulated. We further examined the stress responsiveness of 15 genes by qRT-PCR. A digital northern analysis showed that the PtrDREB17, 18, and 32 genes were highly induced in leaves under cold stress, and the same expression trends were shown by qRT-PCR. Taken together, these observations may lay the foundation for future functional analyses to unravel the biological roles of Populus’ DREB genes.

  8. Transcriptome Profiling of the C. elegans Rb Ortholog Reveals Diverse Developmental Roles

    Kirienko, Natalia V; Fay, David S.


    LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in...

  9. Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States.

    Taniguchi, Takeshi; Imada, Shogo; Acharya, Kumud; Iwanaga, Fumiko; Yamanaka, Norikazu


    Tamarix ramosissima is a tree species that is highly resistant to salt and drought. The Tamarix species survives in a broad range of environmental salt levels, and invades major river systems in southwestern United States. It may affect root-associated bacteria (RB) by increasing soil salts and nutrients. The effects of RB on host plants may vary even under saline conditions, and the relationship may be important for T. ramosissima. However, to the best of our knowledge, there have been no reports relating to T. ramosissima RB and its association with salinity and nutrient levels. In this study, we have examined this association and the effect of arbuscular mycorrhizal colonization of T. ramosissima on RB because a previous study has reported that colonization of arbuscular mycorrhizal fungi affected the rhizobacterial community (Marschner et al., 2001). T. ramosissima roots were collected from five locations with varying soil salinity and nutrient levels. RB community structures were examined by terminal restriction fragment (T-RF) length polymorphism, cloning, and sequencing analyses. The results suggest that RB richness, or the diversity of T. ramosissima, have significant negative relationships with electrical conductivity (EC), sodium concentration (Na), and the colonization of arbuscular mycorrhizal fungi, but have a significant positive relationship with phosphorus in the soil. However, at each T-RF level, positive correlations between the emergence of some T-RFs and EC or Na were observed. These results indicate that high salinity decreased the total number of RB species, but some saline-tolerant RB species multiplied with increasing salinity levels. The ordination scores of nonmetric multidimensional scale analysis of RB community composition show significant relationships with water content, calcium concentration, available phosphorus, and total nitrogen. These results indicate that the RB diversity and community composition of T. ramosissima are affected

  10. Signature splitting inversion and backbending in 80Rb

    He, Chuangye; Wen, Shuxian; Zhu, Lihua; Wu, Xiaoguang; Li, Guangsheng; Zhao, Yue; Yan, Yupeng; Bai, Zhijun; Wu, Yican; Li, Yazhou; Li, Gui; Yan, Shiwei; Oshima, M; Toh, Y; Osa, A; Koizumi, M; Hatsukawa, Y; Matsuda, M; Hagakawa, T


    High spin states of 80Rb are studied via the fusion-evaporation reactions 65Cu+19F, 66Zn+18O and 68Zn+16O with the beam energies of 75 MeV, 76 MeV and 80 MeV, respectively. Twenty-three new states with twenty-eight new \\gamma transitions were added to the previously proposed level scheme, where the second negative-parity band is significantly pushed up to spins of 22^{-} and 15^{-} and two new sidebands are built on the known first negative-parity band. Two successive band crossings with frequencies 0.51 MeV and 0.61 MeV in the \\alpha=0 branch as well as another one in the \\alpha=1 branch of the second negative-parity band are observed for the first time. Signature inversions occur in the positive- and first negative-parity bands at the spins of 11\\hbar and 15\\hbar, respectively. The signature splitting is seen obviously in the second negative-parity band, but the signature inversion is not observed. It is also found that the structure of the two negative-parity bands is similar to that of its isotone ^{82}Y....

  11. A New Rb Lamp Exciter Circuit for Rb atomic clocks and Studies on Transition from Ring to Red mode

    Singh, Savita; Saxena, G M


    In this paper we describe the development of novel RF exciter circuit for electrode less Rb lamp. The lamp exciter circuit is a RF oscillator with a a new configuration operating at 60 to 65 MHz frequency with 3 to 4 watt power. The Rb lamp is used in exciting the ground state hyperfine transitions in Rb atom in a glass cell placed inside a tuned microwave cavity, As the frequency of these hyperfine transitions is very stable it is used in the development of Rb atomic clock by phase locking the oven controlled crystal oscillator (OCXO) to this atomic transition frequency. The details of the Rb lamp exciter are presented in the paper.The Lamp is ideally operated in ring mode as in this mode the linewidth is narrow and there is no self reversal. However, high temperature and RF excitation power may drive the Rb lamp to red mode which gives rise to line broadening and self reversal. It is the experience that mode change from ring to red deteriorates the atomic signal strength and S/N. In this paper the reasons o...

  12. Gene expression and dental enamel structure in developing mouse incisor.

    Sehic, Amer; Risnes, Steinar; Khan, Qalb-E-Saleem; Khuu, Cuong; Osmundsen, Harald


    At the mouse incisor tip the initially differentiated ameloblasts produce a thin, prism-free enamel, while further apically, in the immediate adjacent segment, the enamel thickness increases and the four-layered enamel of mouse incisor is formed. Comparative gene-expression profiling was carried out on RNA isolated from these two segments of incisor tooth germs at embryonic day (E)17.5 and at postnatal days (P)0, 1, 2, and 10 using microarrays to measure messenger RNA (mRNA) and microRNA (miRNA) species present in the segments. Validation of expression data was achieved using real-time reverse transcription-polymerase chain reaction (RT-PCR) and western blotting. Bioinformatic data suggested enhanced cellular apoptosis in the incisal tip segment, which, together with diminished expression of the Amelx and Enam genes, may contribute to the production of the thin enamel seen in this tooth segment. For genes exhibiting higher levels of expression in the adjacent segment where complex enamel is being formed, bioinformatic analysis suggested significant associations with cellular functions involving the actin cytoskeleton, cellular development, morphology, and movement. This is suggested to reflect that ameloblasts with Tomes' process are being organized in transverse rows, facilitating the transverse movement that results in prism decussation in the inner enamel of the adjacent segment. Bioinformatic analysis of miRNA expression data lends support to these suggestions.

  13. Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome.

    Barghi, Neda; Concepcion, Gisela P; Olivera, Baldomero M; Lluisma, Arturo O


    The evolvability of venom components (in particular, the gene-encoded peptide toxins) in venomous species serves as an adaptive strategy allowing them to target new prey types or respond to changes in the prey field. The structure, organization, and expression of the venom peptide genes may provide insights into the molecular mechanisms that drive the evolution of such genes. Conus is a particularly interesting group given the high chemical diversity of their venom peptides, and the rapid evolution of the conopeptide-encoding genes. Conus genomes, however, are large and characterized by a high proportion of repetitive sequences. As a result, the structure and organization of conopeptide genes have remained poorly known. In this study, a survey of the genome of Conus tribblei was undertaken to address this gap. A partial assembly of C. tribblei genome was generated; the assembly, though consisting of a large number of fragments, accounted for 2160.5 Mb of sequence. A large number of repetitive genomic elements consisting of 642.6 Mb of retrotransposable elements, simple repeats, and novel interspersed repeats were observed. We characterized the structural organization and distribution of conotoxin genes in the genome. A significant number of conopeptide genes (estimated to be between 148 and 193) belonging to different superfamilies with complete or nearly complete exon regions were observed, ~60 % of which were expressed. The unexpressed conopeptide genes represent hidden but significant conotoxin diversity. The conotoxin genes also differed in the frequency and length of the introns. The interruption of exons by long introns in the conopeptide genes and the presence of repeats in the introns may indicate the importance of introns in facilitating recombination, evolution and diversification of conotoxins. These findings advance our understanding of the structural framework that promotes the gene-level molecular evolution of venom peptides.

  14. WebScipio: An online tool for the determination of gene structures using protein sequences

    Waack Stephan


    Full Text Available Abstract Background Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. Results WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. Conclusion WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at

  15. UV laser induced desorption of CsI and RbI ion clusters

    Fernández-Lima, F. A.; Ponciano, C. R.; Filho, H. D. Fonseca; Pedrero, E.; Chaer Nascimento, M. A.; da Silveira, E. F.


    Experimental results of laser sputtering of cesium and rubidium iodide secondary ions are presented. A TOF mass spectrometer, operating in linear mode, continuous extraction for positive or negative ions, was used for the analysis of (CsI) nCs +, (CsI) nI -, (RbI) nRb + and (RbI) nI - ion emission as a function of the laser irradiance. Experimental data show that the cluster ion emission yields decrease exponentially with n, for all the laser irradiances applied. Theoretical analysis of the clusters structure was performed using density functional theory at the B3LYP/LACV3P level, for the positive and negative cluster series. A quasi-equilibrium evolution of the clusters is proposed to extract a parameter characteristic of the cluster recombination process: the effective temperature. The hypothesis of the atomic species' recombination (during the expansion of a high density highly ionized cloud) leading to cluster formation is confirmed to some extent in a second set of experiments: the UV laser ablation of a mixed and non-mixed cesium iodide and potassium bromide targets. These experiments show that the emission yields contain contributions from both the recombination process and from the sample stoichiometry, even for high laser irradiances.

  16. Anisotropic upper critical magnetic fields in Rb2Cr3As3 superconductor

    Tang, Zhang-Tu; Liu, Yi; Bao, Jin-Ke; Xi, Chuan-Ying; Pi, Li; Cao, Guang-Han


    Rb2Cr3As3 is a structurally one-dimensional superconductor containing Cr3As3 chains with a superconducting transition temperature of T_c= 4.8 K. Here we report the electrical resistance measurements for Rb2Cr3As3 single crystals, under magnetic fields up to 29.5 T and at temperatures down to 0.36 K, from which the upper critical fields, Hc2(T) , can be obtained in a broad temperature range. For field parallel to the Cr3As3 chains, Hc2\\Vert (T) is paramagnetically limited with an initial slope of μ0 dHc2\\Vert /dT\\vert Tc=-16 T K-1 and a zero-temperature upper critical field of μ0Hc2\\Vert (0)= 17.5 T. For field perpendicular to the Cr3As3 chains, however, Hc2\\bot(T) is only limited by orbital pair-breaking effect with μ0 dHc2\\perp /dT\\vert Tc=-3 T K-1 . As a consequence, the anisotropy γH=Hc2\\Vert /Hc2\\bot decreases sharply near T c and reverses below 2 K. Remarkably, the low-temperature Hc2\\bot(T) down to 0.075 Tc remains to increase linearly up to over three times the Pauli paramagnetic limit, which strongly suggests dominant spin-triplet superconductivity in Rb2Cr3As3.

  17. Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme

    Gu Yong Q


    Full Text Available Abstract Background Among the dietary essential amino acids, the most severely limiting in the cereals is lysine. Since cereals make up half of the human diet, lysine limitation has quality/nutritional consequences. The breakdown of lysine is controlled mainly by the catabolic bifunctional enzyme lysine ketoglutarate reductase - saccharopine dehydrogenase (LKR/SDH. The LKR/SDH gene has been reported to produce transcripts for the bifunctional enzyme and separate monofunctional transcripts. In addition to lysine metabolism, this gene has been implicated in a number of metabolic and developmental pathways, which along with its production of multiple transcript types and complex exon/intron structure suggest an important node in plant metabolism. Understanding more about the LKR/SDH gene is thus interesting both from applied standpoint and for basic plant metabolism. Results The current report describes a wheat genomic fragment containing an LKR/SDH gene and adjacent genes. The wheat LKR/SDH genomic segment was found to originate from the A-genome of wheat, and EST analysis indicates all three LKR/SDH genes in hexaploid wheat are transcriptionally active. A comparison of a set of plant LKR/SDH genes suggests regions of greater sequence conservation likely related to critical enzymatic functions and metabolic controls. Although most plants contain only a single LKR/SDH gene per genome, poplar contains at least two functional bifunctional genes in addition to a monofunctional LKR gene. Analysis of ESTs finds evidence for monofunctional LKR transcripts in switchgrass, and monofunctional SDH transcripts in wheat, Brachypodium, and poplar. Conclusions The analysis of a wheat LKR/SDH gene and comparative structural and functional analyses among available plant genes provides new information on this important gene. Both the structure of the LKR/SDH gene and the immediately adjacent genes show lineage-specific differences between monocots and dicots, and

  18. Synthesis and Characterization of the Rubidium Thiophosphate Rb 6 (PS 5 )(P 2 S 10 ) and the Rubidium Silver Thiophosphates Rb 2 AgPS 4 , RbAg 5 (PS 4 ) 2 and Rb 3 Ag 9 (PS 4 ) 4

    Alahmary, Fatimah S.


    The metal thiophosphates Rb2AgPS4 (2), RbAg5(PS4)2 (3), and Rb3Ag9(PS4)4 (4) were synthesized by stoichiometric reactions, whereas Rb6(PS5)(P2S10) (1) was prepared with excess amount of sulfur. The compounds crystallize as follows: 1 monoclinic, P21/c (no. 14), a = 17.0123(7) Å, b = 6.9102(2) Å, c = 23.179(1) Å, β = 94.399(4)°; 2 triclinic, P ¯ (no. 2), a = 6.600(1) Å, b = 6.856(1) Å, c = 10.943(3) Å, α = 95.150(2)°, β = 107.338(2)°, γ = 111.383(2)°; 3 orthorhombic, Pbca (no. 61), a = 12.607(1) Å, b = 12.612(1) Å, c = 17.759(2) Å; 4 orthorhombic, Pbcm (no. 57), a = 6.3481(2) Å, b = 12.5782(4) Å, c = 35.975(1) Å. The crystal structures contain discrete units, chains, and 3D polyanionic frameworks composed of PS4 tetrahedral units arranged and connected in different manner. Compounds 1-3 melt congruently, whereas incongruent melting behavior was observed for compound 4. 1-4 are semiconductors with bandgaps between 2.3 and 2.6 eV and thermally stable up to 450 °C in an inert atmosphere. Copyright © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Magnetic properties of the RbMnPO4 zeolite-ABW-type material: a frustrated zigzag spin chain.

    Nénert, Gwilherm; Bettis, Jerry; Kremer, Reinhard; Ben Yahia, Hamdi; Ritter, Clemens; Gaudin, Etienne; Isnard, Olivier; Whangbo, Myung-Hwan


    The crystal structure and magnetic properties of the RbMnPO4 zeolite-ABW-type material have been studied by temperature-dependent neutron powder diffraction, low-temperature magnetometry, and heat capacity measurements. RbMnPO4 represents a rare example of a weak ferromagnetic polar material, containing Mn(2+) ions with TN = 4.7 K. The neutron powder diffraction pattern recorded at T = 10 K shows that the compound crystallizes in the chiral and polar monoclinic space group P2(1) (No. 4) with the unit cell parameters: a = 8.94635(9), b = 5.43415(5), and c = 9.10250(8) Å and β = 90.4209(6)°. A close inspection of the crystal structure of RbMnPO4 shows that this material presents two different types of zigzag chains running along the b axis. This is a unique feature among the zeolite-ABW-type materials exhibiting the P2(1) symmetry. At low temperature, RbMnPO4 exhibits a canted antiferromagnetic structure characterized by the propagation vector k1 = 0, resulting in the magnetic symmetry P2(1)'. The magnetic moments lie mostly along the b axis with the ferromagnetic component being in the ac plane. Due to the geometrical frustration present in this system, an intermediate phase appears within the temperature range 4.7-5.1 K characterized by the propagation vector k2 = (kx, 0, kz) with kx/kz ≈ 2. This ratio is reminiscent of the multiferroic phase of the orthorhombic RMnO3 phases (R = rare earth), suggesting that RbMnPO4 could present some multiferroic properties at low temperature. Our density functional calculations confirm the presence of magnetic frustration, which explains this intermediate incommensurate phase. Taking into account the strongest magnetic interactions, we are able to reproduce the magnetic structure observed experimentally at low temperature.

  20. Gene structure, DNA methylation, and imprinted expression of the human SNRPN gene

    Glenn, C.C.; Jong, T.C.; Filbrandt, M.M. [Univ. of Florida College of Medicine, Gainesville, FL (United States)] [and others


    The human SNRPN (small nuclear ribonucleoprotein polypeptide N) gene is one of a gene family that encode proteins involved in pre-mRNA splicing and maps to the smallest deletion region involved in the Prader-Willi syndrome (PWS) within chromosome 15q11-q13. Paternal only expression of SNRPN has previously been demonstrated by use of cell lines from PWS patients (maternal allele only) and Angelman syndrome (AS) patients (paternal allele only). We have characterized two previously unidentified 5{prime} exons of the SNRPN gene and demonstrate that exons -1 and 0 are included in the full-length transcript. This gene is expressed in a wide range of somatic tissues and at high, approximately equal levels in all regions of the brain. Both the first exon of SNRPN (exon -1) and the putative transcription start site are embedded within a CpG island. This CpG island is extensively methylated on the repressed maternal allele and is unmethylated on the expressed paternal allele, in a wide range of fetal and adult somatic cells. This provides a quick and highly reliable diagnostic assay for PWS and AS, which is based on DNA-methylation analysis that has been tested on >100 patients in a variety of tissues. Conversely, several CpG sites {approximately}22 kb downstream of the transcription start site in intron 5 are preferentially methylated on the expressed paternal allele in somatic tissues and male germ cells, whereas these same sites are unmethylated in fetal oocytes. These findings are consistent with a key role for DNA methylation in the imprinted inheritance and subsequent gene expression of the human SNRPN gene. 59 refs., 9 figs., 1 tab.

  1. Structural variation of the ribosomal gene cluster within the class Insecta

    Mukha, D.V.; Sidorenko, A.P.; Lazebnaya, I.V. [Vavilov Institute of General Genetics, Moscow (Russian Federation)] [and others


    General estimation of ribosomal DNA variation within the class Insecta is presented. It is shown that, using blot-hybridization, one can detect differences in the structure of the ribosomal gene cluster not only between genera within an order, but also between species within a genera, including sibling species. Structure of the ribosomal gene cluster of the Coccinellidae family (ladybirds) is analyzed. It is shown that cloned highly conservative regions of ribosomal DNA of Tetrahymena pyriformis can be used as probes for analyzing ribosomal genes in insects. 24 refs., 4 figs.

  2. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    Flores, Kevin B


    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  3. How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes?

    Sawada, Ryusuke; Mitaku, Shigeki


    The exon-intron structure of eukaryotic genes raises a question about the distribution of transmembrane regions in membrane proteins. Were exons that encode transmembrane regions formed simply by inserting introns into preexisting genes or by some kind of exon shuffling? To answer this question, the exon-per-gene distribution was analyzed for all genes in 40 eukaryotic genomes with a particular focus on exons encoding transmembrane segments. In 21 higher multicellular eukaryotes, the percentage of multi-exon genes (those containing at least one intron) within all genes in a genome was high (>70%) and with a mean of 87%. When genes were grouped by the number of exons per gene in higher eukaryotes, good exponential distributions were obtained not only for all genes but also for the exons encoding transmembrane segments, leading to a constant ratio of membrane proteins independent of the exon-per-gene number. The positional distribution of transmembrane regions in single-pass membrane proteins showed that they are generally located in the amino or carboxyl terminal regions. This nonrandom distribution of transmembrane regions explains the constant ratio of membrane proteins to the exon-per-gene numbers because there are always two terminal (i.e., the amino and carboxyl) regions - independent of the length of sequences.

  4. The IQD gene family in soybean: structure, phylogeny, evolution and expression.

    Lin Feng

    Full Text Available Members of the plant-specific IQ67-domain (IQD protein family are involved in plant development and the basal defense response. Although systematic characterization of this family has been carried out in Arabidopsis, tomato (Solanum lycopersicum, Brachypodium distachyon and rice (Oryza sativa, systematic analysis and expression profiling of this gene family in soybean (Glycine max have not previously been reported. In this study, we identified and structurally characterized IQD genes in the soybean genome. A complete set of 67 soybean IQD genes (GmIQD1-67 was identified using Blast search tools, and the genes were clustered into four subfamilies (IQD I-IV based on phylogeny. These soybean IQD genes are distributed unevenly across all 20 chromosomes, with 30 segmental duplication events, suggesting that segmental duplication has played a major role in the expansion of the soybean IQD gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the GmIQD family primarily underwent purifying selection. Microsynteny was detected in most pairs: genes in clade 1-3 might be present in genome regions that were inverted, expanded or contracted after the divergence; most gene pairs in clade 4 showed high conservation with little rearrangement among these gene-residing regions. Of the soybean IQD genes examined, six were most highly expressed in young leaves, six in flowers, one in roots and two in nodules. Our qRT-PCR analysis of 24 soybean IQD III genes confirmed that these genes are regulated by MeJA stress. Our findings present a comprehensive overview of the soybean IQD gene family and provide insights into the evolution of this family. In addition, this work lays a solid foundation for further experiments aimed at determining the biological functions of soybean IQD genes in growth and development.

  5. RbCa2Nb3O10 from X-ray powder data

    Zhen-Hua Liang; Kai-Bin Tang; Qian-Wang Chen; Hua-Gui Zheng


    Rubidium dicalcium triniobate(V), RbCa2Nb3O10, has been synthesized by solid-state reaction and its crystal structure refined from X-ray powder diffraction data using Rietveld analysis. The compound is a three-layer perovskite Dion–Jacobson phase with the perovskite-like slabs derived by termination of the three-dimensional CaNbO3 perovskite structure along the ab plane. The rubidium ions (4/mmm symmetry) are located in the interstitial space.

  6. Bottleneck genes and community structure in the cell cycle network of S. pombe.

    Cécile Caretta-Cartozo


    Full Text Available The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in their results. We introduce a network in which the weight of each link is a function of the phase difference between the expression peaks of two genes. The analysis of the stability of the clustering through the computation of an entropy parameter reveals a structure made of four clusters, the first one corresponding to a robustly connected M-G1 component, the second to genes in the S phase, and the third and fourth to two G2 components. They are separated by bottleneck structures that appear to correspond to cell cycle checkpoints. We identify a number of genes that are located on these bottlenecks. They represent a novel group of cell cycle regulatory genes. They all show interesting functions, and they are supposed to be involved in the regulation of the transition from one phase to the next. We therefore present a comparison of the available studies on the fission yeast cell cycle and a general statistical bioinformatics methodology to find bottlenecks and gene community structures based on recent developments in network theory.

  7. $\\gamma$ -spectroscopy of n-rich $^{95,96}$Rb nuclei by the incomplete fusion reaction of $^{94}$Kr on $^{7}$Li

    We propose an experiment with MINIBALL coupled to T-REX to investigate n-rich $^{95,96}$Rb nuclei by the incomplete fusion reaction of $^{94}$Kr on $^{7}$Li. The nuclei of interest will be populated by transfer of a triton into $^{94}$Kr, forming the excited $^{97}$Rb nucleus, followed by the emission of an alpha particle, which will be detected in the Si telescopes of T-REX. The $^{97}$Rb product will evaporate 1 or 2 (with the highest probability) neutrons leading to $^{96}$Rb or $^{95}$Rb, respectively. The aim of the experiment is twofold: \\\\ i) to perform a $\\gamma$- spectroscopy study of $^{95,96}$Rb nuclei with N=58,59, the structure of which is of particular interest in investigating the transition towards stable deformation at N=60, \\\\ ii) to acquire experience in using incomplete fusion reactions with the weakly bound $^{7}$Li target, in order to perform, at a later stage with HIE-ISOLDE, similar measurements induced by n-rich radioactive beams of Sn and Hg, for which at least 5 MeV/nucleon are need...

  8. Functional genomics and structural biology in the definition of gene function.

    Hrmova, Maria; Fincher, Geoffrey B


    By mid-2007, the three-dimensional (3D) structures of some 45,000 proteins have been solved, over a period where the linear structures of millions of genes have been defined. Technical challenges associated with X-ray crystallography are being overcome and high-throughput methods both for crystallization of proteins and for solving their 3D structures are under development. The question arises as to how structural biology can be integrated with and adds value to functional genomics programs. Structural biology will assist in the definition of gene function through the identification of the likely function of the protein products of genes. The 3D information allows protein sequences predicted from DNA sequences to be classified into broad groups, according to the overall 'fold', or 3D shape, of the protein. Structural information can be used to predict the preferred substrate of a protein, and thereby greatly enhance the accurate annotation of the corresponding gene. Furthermore, it will enable the effects of amino acid substitutions in enzymes to be better understood with respect to enzyme function and could thereby provide insights into natural variation in genes. If the molecular basis of transcription factor-DNA interactions were defined through precise 3D knowledge of the protein-DNA binding site, it would be possible to predict the effects of base substitutions within the motif on the specificity and/or kinetics of binding. In this chapter, we present specific examples of how structural biology can provide valuable information for functional genomics programs.

  9. Structural analysis of TL genes of the mouse.

    Obata, Y; Chen, Y T; Stockert, E; Old, L J


    Three Tla region-specific probes have been generated from the BALB/c genomic cosmid clone C6.3. One probe, pTL1, corresponds to 3' sequences of a thymus leukemia (TL)-encoding gene, whereas pTL2 and pTL3 detect noncoding flanking sequences. The TL specificity of pTL1 was demonstrated by studies of RNA from thymocytes of TL+ and TL- mouse strains and from TL+ and TL- leukemias; presence/absence of pTL1+ transcripts correlated with presence/absence of TL antigens detected serologically. Nine Tl...

  10. Characterization of Genetic Structures of the QepA3 Gene in Clinical Isolates of Enterobacteriaceae

    Dongguo eWang


    Full Text Available QepA is one of the genes that confer quinolone resistance in bacteria. The aim of this study was to analyze the genetic structures of plasmids that carry a qepA3, a recently discovered allele of qepA in Enterobacteriaceae clinical isolates. 656 non-redundant Enterobacteriaceae clinical isolates were screened for the qepA3 gene and five isolated were identified to carry the gene. Plasmids were isolated from these isolates and were found to increase antibiotic resistance once the plasmids were transferred to Escherichia coli. These plasmids were subcloned and sequenced to analyze the genetic structures surrounding the the qepA3 gene. The results showed that the five plasmids had different genetic structures; one of qepA3-containning isolates had either the blaCTX-M-14 or blaTEM-12 gene in place of the blaTEM-1 gene. The structures of both pKP3764 and pECL3786 have not been previously described. In comparison with pHPA, there were a number of changes in DNA sequences up- and down-stream the qepA3 gene. These findings provide better understanding of the genetic variations in qepA3 and would be useful for diagnosis and control of quinolone resistance in clinical settings.

  11. Characterization of genetic structures of the QepA3 gene in clinical isolates of Enterobacteriaceae

    Wang, Dongguo; Huang, Xitian; Chen, Jiayu; Mou, Yonghua; Li, Haijun; Yang, Liqin


    QepA is one of the genes that confer quinolone resistance in bacteria. The aim of this study was to analyze the genetic structures of plasmids that carry a qepA3, a recently discovered allele of qepA in Enterobacteriaceae clinical isolates. 656 non-redundant Enterobacteriaceae clinical isolates were screened for the qepA3 gene and five isolates were identified to carry the gene. Plasmids were isolated from these isolates and were found to increase antibiotic resistance once the plasmids were transferred to Escherichia coli. These plasmids were subcloned and sequenced to analyze the genetic structures surrounding the qepA3 gene. The results showed that the five plasmids had different genetic structures; two of the qepA3-containning isolates had either the blaCTX-M-14 or blaTEM-12 gene instead of the blaTEM-1 gene. The structures of both pKP3764 and pECL3786 have not been previously described. In comparison with pHPA, there were a number of changes in DNA sequences up- and down-stream of the qepA3 gene. These findings provide better understanding of the genetic variations in qepA3 and would be useful for diagnosis and control of quinolone resistance in clinical settings. PMID:26528280

  12. BLCAP arrests G₁/S checkpoint and induces apoptosis through downregulation of pRb1 in HeLa cells.

    Zhao, Min; Zhang, Li; Qiu, Xiaoping; Zeng, Fanyu; Chen, Wen; An, Yuehui; Hu, Bicheng; Wu, Xufeng; Wu, Xinxing


    BLCAP (bladder cancer-associated protein) gene exhibited tumor suppressor function in different tumors and is regarded as a candidate tumor suppressor gene; however, the mechanism by which BLCAP exerts its function remains elusive. This study investigated the functional association between BLCAP and proliferation or apoptosis in cervical cancer cells, to identify the functional motifs of BLCAP. The BLCAP-shRNA expression vector based on pRNA-U6.1/Hygro plasmid was used to specifically inhibit BLCAP activity in HeLa cells. The optimal shRNA plasmid was selected to knock down BLCAP expression and the biological effects were investigated. The effects on cell cycle and apoptosis were detected by flow cytometric or Annexin V-FITC staining analysis. The gene expression profiles of HeLa cells transfected with blcap-wt and BLCAP-shRNA were analyzed using human signal pathway gene Oligochips. The levels of protein expression and interaction of BLCAP with Rb1 proteins were determined by western blotting and Co-IP assays. The site-specific mutagenesis assay was used to identify amino acid residues important for BLCAP. Significantly differentially expressed genes were found by gene Oligo chips analysis. These genes were all correlated with proliferation, cell cycle and apoptosis. The results of western blotting and Co-IP assays confirmed that overexpression of BLCAP could interact with Rb1 and inhibit Rb1 phosphorylation. Further investigation revealed that SAXX mutation in the key regions of BLCAP suppressed the function of BLCAP and significantly increased the level of phosphorylated Rb1 protein. Here our findings suggested that the functional association of BLCAP and Rb1 might play important roles in proliferation and apoptosis of HeLa cells. It suggested that BLCAP could be a novel therapeutic target for cervical cancer.

  13. Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence.

    Jagielska, Elżbieta; Płucienniczak, Andrzej; Dąbrowska, Magdalena; Dowierciał, Anna; Rode, Wojciech


    Thymidylate synthase is a housekeeping gene, designated ancient due to its role in DNA synthesis and ubiquitous phyletic distribution. The genomic sequences were characterized coding for thymidylate synthase in two species of the genus Trichinella, an encapsulating T. spiralis and a non-encapsulating T. pseudospiralis. Based on the sequence of parasitic nematode Trichinella spiralis thymidylate synthase cDNA, PCR techniques were employed. Each of the respective gene structures encompassed 6 exons and 5 introns located in conserved sites. Comparison with the corresponding gene structures of other eukaryotic species revealed lack of common introns that would be shared among selected fungi, nematodes, mammals and plants. The two deduced amino acid sequences were 96% identical. In addition to the thymidylate synthase gene, the intron-less retrocopy, i.e. a processed pseudogene, with sequence identical to the T. spiralis gene coding region, was found to be present within the T. pseudospiralis genome. This pseudogene, instead of the gene, was confirmed by RT-PCR to be expressed in the parasite muscle larvae. Intron load, as well as distribution of exon and intron phases in thymidylate synthase genes from various sources, point against the theory of gene assembly by the primordial exon shuffling and support the theory of evolutionary late intron insertion into spliceosomal genes. Thymidylate synthase pseudogene expressed in T. pseudospiralis muscle larvae is designated a retrogene.

  14. Silencing structural and nonstructural genes in baculovirus by RNA interference.

    Flores-Jasso, C Fabian; Valdes, Victor Julian; Sampieri, Alicia; Valadez-Graham, Viviana; Recillas-Targa, Felix; Vaca, Luis


    We review several aspects of RNAi and gene silencing with baculovirus. We show that the potency of RNAi in Spodoptera frugiperda (Sf21) insect cells correlates well with the efficiency of transfection of the siRNA. Using a fluorescein-labeled siRNA we found that the siRNA localized in areas surrounding the endoplasmic reticulum (ER). Both long (700 nucleotides long) and small ( approximately 25 nucleotides long) interfering RNAs were equally effective in initiating RNA interference (RNAi), and the duration of the interfering effect was indistinguishable. Even though RNAi in Sf21 cells is very effective, in vitro experiments show that these cells fragment the long dsRNA into siRNA poorly, when compared to HEK cells. Finally, we show that in vivo inhibition of baculovirus infection with dsRNA homologous to genes that are essential for baculovirus infectivity depends strongly on the amount of dsRNA used in the assays. Five hundred nanogram of dsRNA directly injected into the haemolymph of insects prevent animal death to over 95%. In control experiments, over 96% of insects not injected with dsRNA or injected with an irrelevant dsRNA died within a week. These results demonstrate the efficiency of dsRNA for in vivo prevention of a viral infection by virus that is very cytotoxic and lytic in animals.

  15. The immunoglobulin genes: structure and specificity in chronic lymphocytic leukemia.

    Tobin, Gerard


    The rearrangement of the immunoglobulin genes (IG) provides a large diversity of B-cell receptors conformations and allows the immune system to respond differently to foreign antigens. In chronic lymphocytic leukemia (CLL), there are a restricted number of stereotyped B-cell receptors rearranged by the tumor B-cells between CLL patients. These subsets with stereotyped receptors appear to have clinical implications, for example cases that rearrange the IGHV3-21 gene display poor clinical prognosis. The number of subsets with stereotyped receptors has been reported at a frequency of over 20% of CLL cases; however, the specificities of these receptors are still not clearly defined. Reactivity to epitopes from bacterial antigen, cytoskeleton components such as vimentin, and antigens on viable and apoptotic T-cell have been proposed. The role of antigen in CLL development is currently being more clearly defined with identification of stereotyped receptors, and their antigen specificity and the continued role antigen stimulation plays in CLL disease will be an important question in the future.

  16. In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure

    Yang Hangxing


    Full Text Available Abstract Background Compactness of highly/broadly expressed genes in human has been explained as selection for efficiency, regional mutation biases or genomic design. However, highly expressed genes in flowering plants were shown to be less compact than lowly expressed ones. On the other hand, opposite facts have also been documented that pollen-expressed Arabidopsis genes tend to contain shorter introns and highly expressed moss genes are compact. This issue is important because it provides a chance to compare the selectionism and the neutralism views about genome evolution. Furthermore, this issue also helps to understand the fates of introns, from the angle of gene expression. Results In this study, I used expression data covering more tissues and employ new analytical methods to reexamine the correlations between gene expression and gene structure for two flowering plants, Arabidopsis thaliana and Oryza sativa. It is shown that, different aspects of expression pattern correlate with different parts of gene sequences in distinct ways. In detail, expression level is significantly negatively correlated with gene size, especially the size of non-coding regions, whereas expression breadth correlates with non-coding structural parameters positively and with coding region parameters negatively. Furthermore, the relationships between expression level and structural parameters seem to be non-linear, with the extremes of structural parameters possibly scale as power-laws or logrithmic functions of expression levels. Conclusion In plants, highly expressed genes are compact, especially in the non-coding regions. Broadly expressed genes tend to contain longer non-coding sequences, which may be necessary for complex regulations. In combination with previous studies about other plants and about animals, some common scenarios about the correlation between gene expression and gene structure begin to emerge. Based on the functional relationships between

  17. The vertebrate RCAN gene family: novel insights into evolution, structure and regulation.

    Eva Serrano-Candelas

    Full Text Available Recently there has been much interest in the Regulators of Calcineurin (RCAN proteins which are important endogenous modulators of the calcineurin-NFATc signalling pathway. They have been shown to have a crucial role in cellular programmes such as the immune response, muscle fibre remodelling and memory, but also in pathological processes such as cardiac hypertrophy and neurodegenerative diseases. In vertebrates, the RCAN family form a functional subfamily of three members RCAN1, RCAN2 and RCAN3 whereas only one RCAN is present in the rest of Eukarya. In addition, RCAN genes have been shown to collocate with RUNX and CLIC genes in ACD clusters (ACD21, ACD6 and ACD1. How the RCAN genes and their clustering in ACDs evolved is still unknown. After analysing RCAN gene family evolution using bioinformatic tools, we propose that the three RCAN vertebrate genes within the ACD clusters, which evolved from single copy genes present in invertebrates and lower eukaryotes, are the result of two rounds of whole genome duplication, followed by a segmental duplication. This evolutionary scenario involves the loss or gain of some RCAN genes during evolution. In addition, we have analysed RCAN gene structure and identified the existence of several characteristic features that can be involved in RCAN evolution and gene expression regulation. These included: several transposable elements, CpG islands in the 5' region of the genes, the existence of antisense transcripts (NAT associated with the three human genes, and considerable evidence for bidirectional promoters that regulate RCAN gene expression. Furthermore, we show that the CpG island associated with the RCAN3 gene promoter is unmethylated and transcriptionally active. All these results provide timely new insights into the molecular mechanisms underlying RCAN function and a more in depth knowledge of this gene family whose members are obvious candidates for the development of future therapies.

  18. lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein.

    Davison, Ewa M; Harrison, Melissa M; Walhout, Albertha J M; Vidal, Marc; Horvitz, H Robert


    Ras-mediated vulval development in C. elegans is inhibited by the functionally redundant sets of class A, B, and C synthetic Multivulva (synMuv) genes. Three of the class B synMuv genes encode an Rb/DP/E2F complex that, by analogy with its mammalian and Drosophila counterparts, has been proposed to silence genes required for vulval specification through chromatin modification and remodeling. Two class A synMuv genes, lin-15A and lin-56, encode novel nuclear proteins that appear to function as a complex. We show that a third class A synMuv gene, lin-8, is the defining member of a novel C. elegans gene family. The LIN-8 protein is nuclear and can interact physically with the product of the class B synMuv gene lin-35, the C. elegans homolog of mammalian Rb. LIN-8 likely acts with the synMuv A proteins LIN-15A and LIN-56 in the nucleus, possibly in a protein complex with the synMuv B protein LIN-35 Rb. Other LIN-8 family members may function in similar complexes in different cells or at different stages. The nuclear localization of LIN-15A, LIN-56, and LIN-8, as well as our observation of a direct physical interaction between class A and class B synMuv proteins, supports the hypothesis that the class A synMuv genes control vulval induction through the transcriptional regulation of gene expression.

  19. Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii.

    Hamilton, Trinity L; Jacobson, Marty; Ludwig, Marcus; Boyd, Eric S; Bryant, Donald A; Dean, Dennis R; Peters, John W


    Northern analysis was employed to investigate mRNA produced by mutant strains of Azotobacter vinelandii with defined deletions in the nif structural genes and in the intergenic noncoding regions. The results indicate that intergenic RNA secondary structures effect the differential accumulation of transcripts, supporting the high Fe protein-to-MoFe protein ratio required for optimal diazotrophic growth.

  20. The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation.

    Gu, Wanjun; Xu, Yuming; Xie, Xueying; Wang, Ting; Ko, Jae-Hong; Zhou, Tong


    Recent studies have suggested that the secondary structure of the 5' untranslated region (5' UTR) of messenger RNA (mRNA) is important for microRNA (miRNA)-mediated gene regulation in humans. mRNAs that are targeted by miRNA tend to have a higher degree of local secondary structure in their 5' UTR; however, the general role of the 5' UTR in miRNA-mediated gene regulation remains unknown. We systematically surveyed the secondary structure of 5' UTRs in both plant and animal species and found a universal trend of increased mRNA stability near the 5' cap in mRNAs that are regulated by miRNA in animals, but not in plants. Intra-genome comparison showed that gene expression level, GC content of the 5' UTR, number of miRNA target sites, and 5' UTR length may influence mRNA structure near the 5' cap. Our results suggest that the 5' UTR secondary structure performs multiple functions in regulating post-transcriptional processes. Although the local structure immediately upstream of the start codon is involved in translation initiation, RNA structure near the 5' cap site, rather than the structure of the full-length 5' UTR sequences, plays an important role in miRNA-mediated gene regulation.

  1. SUSY effects in Rb: Revisited under current experimental constraints

    Su, Wei; Yang, Jin Min


    In this note we revisit the SUSY effects in Rb under current experimental constraints including the LHC Higgs data, the B-physics measurements, the dark matter relic density and direct detection limits, as well as the precision electroweak data. We first perform a scan to figure out the currently allowed parameter space and then display the SUSY effects in Rb. We find that although the SUSY parameter space has been severely restrained by current experimental data, both the general MSSM and the natural-SUSY scenario can still alter Rb with a magnitude sizable enough to be observed at future Z-factories (ILC, CEPC, FCC-ee, Super Z-factory) which produce 109-1012Z-bosons. To be specific, assuming a precise measurement δRb = 2.0 ×10-5 at FCC-ee, we can probe a right-handed stop up to 530 GeV through chargino-stop loops, probe a sbottom to 850 GeV through neutralino-sbottom loops and a charged Higgs to 770 GeV through the Higgs-top quark loops for a large tan ⁡ β. The full one-loop SUSY correction to Rb can reach 1 ×10-4 in natural SUSY and 2 ×10-4 in the general MSSM.

  2. Low-frequency excitations in Rb{sub 3}C{sub 60} and Rb{sub 6}C{sub 60}

    Schober, H. [Institut Max von Laue - Paul Langevin, 38 - Grenoble (France); Renker, B. [INFP, Forschungszentrum Karlsruhe, D-76021 Karlsruhe (Germany); Gompf, F. [INFP, Forschungszentrum Karlsruhe, D-76021 Karlsruhe (Germany)


    We present inelastic neutron scattering results for Rb{sub 3}C{sub 60} and Rb{sub 6}C{sub 60} covering the energy region from 0.5 to 14 meV. The different contributions to the spectra (translational, libronic, Rb-vibrations) are discussed on the basis of their Q and temperature dependence. In superconducting Rb{sub 3}C{sub 60} the scattering intensity observed in the range from 1.5 to 3.5 meV changes anomalously with temperature. No such behaviour is found in insulating Rb{sub 6}C{sub 60}. (orig.).

  3. Mobile genes in the human microbiome are structured from global to individual scales.

    Brito, I L; Yilmaz, S; Huang, K; Xu, L; Jupiter, S D; Jenkins, A P; Naisilisili, W; Tamminen, M; Smillie, C S; Wortman, J R; Birren, B W; Xavier, R J; Blainey, P C; Singh, A K; Gevers, D; Alm, E J


    Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

  4. Structural comparison and chromosomal localization of the human and mouse IL-13 genes

    McKenzie, A.N.J.; Sato, A.; Doyle, E.L.; Zurawski, G. (DNAX Research Institute of Cellular and Molecular Biology, Palo Alto, CA (United States)); Li, X.; Milatovich, A.; Francke, U. (Stanford Univ. Medical School, CA (United States)); Largaespada, D.A.; Copeland, N.G.; Jenkins, N.A. (National Cancer Institute, Frederick, MD (United States))


    The genomic structure of the recently described cytokine IL-13 has been determined for both human and mouse genes. The nucleotide sequence of a 4.6-kb DNA segment of the human gene is described. The human IL-13 gene (IL 13) occurs as a single copy in the haploid genome and maps to human chromosome 5. A 4.3-kb DNA fragment of the mouse IL-13 gene (Il 13) has been sequenced and found to occur as a single copy, mapping to mouse chromosome 11. Intrachromosomal mapping studies revealed that both genes contain four exons and three introns and show a high degree of sequence identify throughout their length. Potential recognition sequences for transcription factors that are present in the 5'-flanking region and are conserved between both genes include IFN-responsive elements, binding sites for AP-1, AP-2, and AP-3, an NF-lL 6 site, and a TATA-like sequence. Both genes map to chromosomal locations adjacent to genes encoding other cytokines, including IL-3, GM-CSF, IL-5, and IL-4 suggesting that IL-13 is another member of this cytokine gene family that may have arisen by gene duplication. 26 refs., 5 figs., 3 tabs.

  5. Development of the new RB26DETT engine. Shingata RB26DETT engine no kaihatsu

    Ura, S.; Nakamura, K.; Fujita, H.; Eto, T.; Yamanaka, J. (Nissan Motor Co. Ltd., Tokyo (Japan))


    This paper introduces the RB26DETT engine which was developed by Nissan Motor Co., Ltd., for use in the new high-performance Skyline GT-R sports coupe. This is 2.6 liter DOHC twin-turbo engine developed for the aim to built the world {prime} s best mass-produced in-line 6-cylinder engine by integrating the most advanced techniques. It features the adaptation of twin ceramic turbochargers which vastly reduce the interference between exhaust gas flows, and the equipment of large-capacity air-cooled intercooler system which greatly improves the cooling capacity. Other features include the applying of six throttle butterflies for improved intake air response during acceleration and a lighter weight valvetrain. As the result, high output, excellent throttle response and an impressive rotation speed were attained and world-top-class performance surpassing that of sports car engines was obtained. 14 figs., 3 tabs.

  6. ZmcrtRB3 Encodes a Carotenoid Hydroxylase that Affects the Accumulation of α-carotene in Maize Kernel

    Yi Zhou; Yingjia Han; Zhigang Li; Yang Fu; Zhiyuan Fu; Shutu Xu; Jiansheng Li; Jianbing Yan; Xiaohong Yang


    α-carotene is one of the important components of pro-vitamin A,which is able to be converted into vitamin A in the human body.One maize (Zea mays L.) ortholog of carotenoid hydroxylases in Arabidopsis thaliana,ZmcrtRB3,was cloned and its role in carotenoid hydrolyzations was addressed.ZmcrtRB3 was mapped in a quantitative trait locus (QTL) cluster for carotenoid-related traits on chromosome 2 (bin 2.03) in a recombinant inbred line (RIL) population derived from By804 and B73.Candidate-gene association analysis identified 18 polymorphic sites in ZmcrtRB3 significantly associated with one or more carotenoid-related traits in 126 diverse yellow maize inbred lines.These results indicate that the enzyme ZmcrtRB3 plays a role in hydrolyzing both α- andβ-carotenes,while polymorphisms in ZmcrtRB3 contributed more variation in α-carotene than that inβ-carotene.Two single nucleotide polymorphisms (SNPs),SNP1343 in 5'untranslated region and SNP2172 in the second intron,consistently had effects on α-carotene content and composition with explained phenotypic variations ranging from 8.7% to 34.8%.There was 1.7- to 3.7-fold change between the inferior and superior haplotype for α-carotene content and composition.Thus,SNP1343 and SNP2172 are potential polymorphic sites to develop functional markers for applying marker-assisted selection in the improvement of pro-vitamin A carotenoids in maize kernels.

  7. Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

    Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E


    Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of

  8. Structure and evolution of the mouse pregnancy-specific glycoprotein (Psg gene locus

    Okumura Katsuzumi


    Full Text Available Abstract Background The pregnancy-specific glycoprotein (Psg genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea gene family, which is a member of the immunoglobulin gene (Ig superfamily. In rodents and primates, but not in artiodactyls (even-toed ungulates / hoofed mammals, there have been independent expansions of the Psg gene family, with all members expressed exclusively in placental trophoblast cells. For the mouse Psg genes, we sought to determine the genomic organisation of the locus, the expression profiles of the various family members, and the evolution of exon structure, to attempt to reconstruct the evolutionary history of this locus, and to determine whether expansion of the gene family has been driven by selection for increased gene dosage, or diversification of function. Results We collated the mouse Psg gene sequences currently in the public genome and expressed-sequence tag (EST databases and used systematic BLAST searches to generate complete sequences for all known mouse Psg genes. We identified a novel family member, Psg31, which is similar to Psg30 but, uniquely amongst mouse Psg genes, has a duplicated N1 domain. We also identified a novel splice variant of Psg16 (bCEA. We show that Psg24 and Psg30 / Psg31 have independently undergone expansion of N-domain number. By mapping BAC, YAC and cosmid clones we described two clusters of Psg genes, which we linked and oriented using fluorescent in situ hybridisation (FISH. Comparison of our Psg locus map with the public mouse genome database indicates good agreement in overall structure and further elucidates gene order. Expression levels of Psg genes in placentas of different developmental stages revealed dramatic differences in the developmental expression profile of individual family members. Conclusion We have combined existing information, and provide new information concerning the evolution of mouse Psg exon organization, the mouse

  9. Diffusion of Rb atoms in paraffin - coated resonant vapor cells

    Atutov, S N; Plekhanov, A I; Sorokin, V A; Yakovlev, A V


    We present the results of a study of the diffusion of Rb atoms in paraffin - coated resonant vapor cells. We have modeled the Rb diffusion both in the cell and in the coating, assuming that the main loss of Rb atoms is due to the physical absorption of the atoms by the glass substrate. It is demonstrated that the equilibrium atomic density in the cell is a monotonic function of the thickness of the paraffin coating: the density increases with an increase in the thickness of the coating. The diffusion coefficient for rubidium in paraffin thin films has been determined to be equal to 4,7*10^-7 cm^2/s. The results of the experiment might be useful for a better understanding of the details involved in the processes of the interaction of alkali atoms with a paraffin coating.

  10. \\textit{Ab initio} study of reactive collisions between Rb($^{2}S$) or Rb($^{2}P$) and OH$^{-}$($^{1}\\Sigma^{+}$)

    Kas, Milaim; Liévin, Jacques; Vaeck, Nathalie


    A theoretical rate constant for the associative detachment reaction Rb($^{2}S$)$+$OH$^{-}$($^{1}\\Sigma^{+}$)$\\rightarrow \\,$ RbOH($^{1}\\Sigma^{+}$)$+\\,e^{-}$ of 4$\\,\\times$10$^{-10}$cm$^{3}$s$^{-1}$ at 300 K has been calculated. This result agrees with the experimental rate constant of 2$^{+2}_{-1}\\,\\times10^{-10}$cm$^{3}$s$^{-1}$ obtained by Deiglmayr \\textit{et al.} (Phys. Rev. A 86, 2012) for a temperature between 200 K and 600 K. A Langevin-based dynamics which depends on the crossing point between the anion (RbOH$^{-}$) and neutral (RbOH) potential energy surfaces has been used. The calculation were performed using the ECP28MDF effective core potential to describe the rubidium atom at the CCSD(T) level of theory and extended basis sets. The effect of ECPs and basis set on the height of the crossing point, and hence the rate constant, has been investigated. The temperature dependence of the latter is also discussed. Preliminary work on the potential energy surface for the excited reaction channel Rb($^{2}...

  11. Gene structural analysis and expression of human renal dipeptidase

    Satoh, Susumu; Ohtsuka, Kazuyuki; Keida, Yuriko; Kusunoki, Chihiro; Niwa, Mineo; Kohsaka, Masanobu (Fujisawa Pharmaceutical Company, Ltd., Osaka (Japan)); Konta, Yoshiyuki (Hirosaki Univ. (Japan))

    Human renal dipeptidase cDNA and genomic DNA were isolated from human kidney cDNA and genomic libraries, respectively. The human renal dipeptidase gene has a total length of approximately 6 kb and consists of ten exons and nine introns. The exons and cDNA each encode the 411 amino acid residues of the precursor protein, including 16 amino acid residues of signal sequence and a hydrophobic carboxyl terminal sequence for the attachment of a phosphatidylinositol glycan. Although the cDNA was slightly different from the cDNA reported by Adachi et al. (1990), the differences observed suggest, by comparison with human genomic DNA, that it may not represent an allelic variant but a cloning artifact. The recombinant human renal dipeptidase was produced on the surface of transfected L929 cells and had the same character as native renal dipeptidase. Northern blotting hybridization analysis showed that renal dipeptidase mRNA is only transcribed in kidney. 21 refs., 5 figs., 2 tabs.

  12. Gene structure and evolution of transthyretin in the order Chiroptera.

    Khwanmunee, Jiraporn; Leelawatwattana, Ladda; Prapunpoj, Porntip


    Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested.

  13. Phosphorylation of a specific cdk site in E2F-1 affects its electrophoretic mobility and promotes pRB-binding in vitro

    Peeper, D S; Keblusek, P; Helin, K;


    of the retinoblastoma gene (pRB). We find that E2F-1 proteins are heterogeneously phosphorylated in insect cells, as a result of which they migrate as a doublet on SDS-polyacrylamide gels. This electrophoretic shift is shown to be dependent upon specific phosphorylation of E2F-1 on serine-375 (S375), near the p...... affinity of pRB in vitro. These results suggest a novel way of regulating E2F-1 activity, namely by cell-cycle-dependent phosphorylation of this transcription factor....

  14. [Study on the Effects of Ginsenoside Rb1 on DPPC Bilayers by Using Thermo-Raman Spectrum and DSC].

    Hui, Ge; Liu, Wei; Zhang, Jing-zhou; Zhou, Tie-li; Wang, Si-ming; Zhao, Yu; Zhao, Bing


    The research on the interactions between Ginsenosides and biomembranes plays a crucial role in thorough understanding the pharmacological activity and biologyical effect of Chinese medicine Panax ginseng. With the bilayer structure, DPPC often serves as an simulation model of the cell membrane to study the role of drug molecules and cell membranes. Ginsenoside Rb1, one of the most important components of Panaxginseng, playing the significant roles of pharmacological effects and biological properties. Raman and differential scanning calorimetry (DSC) are respectively a powerful tool for discussing the molecular interaction, and a kind of general technology by which researching the bilayer monomer structures and its interactions with drug molecules. However, rarely research reports on the interactions between drug molecules and biomembranes by means of both technologies above. In this paper, the influence of ginsenoside monomer Rb1 on DPPC membrane bilayers was investigated by thermo-Raman and DSC. In Raman spectra, the changes of DPPC molecule have been observed before and after interacted with ginsenoside Rb1, the data analysis indicates three aspects: the O-C-C-N+ polar head group skeleton, C-C stretching vibration area, and the C-H bond stretching vibrarion in terminated methyl group of alkyl chains. The results showed that ginsenoside Rb1 molecule with certain concentration has not changed the gauche conformation of the polar head backbone group in DPPC bilayers, the order of the internal molecular chain and the lateral chain-chain packing have been decreased as the temperature increased, the lateral disposed disorder has been increased. The changes of some thermodynamic constants obtained by DSC experiment such as phase transition temperature (Tm), the temperature at which the transition is half completed (ΔT1/2), and the transition enthalpy normalized per mol of DPPC (AH) have been showed further results of the thermo Raman experiments, with increasing the

  15. Sequence and secondary structure of the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis.

    Krakowetz, Chantel N; Chilton, Neil B


    The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America.

  16. Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure

    de Groot, Saskia; Mailund, Thomas; Hein, Jotun


    Motivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading frames. Since one amino acid is encoded by a triplet of nucleic acids, up to three genes may be coded...... allows for coding in unidirectional nested and overlapping reading frames, to annotate two homologous aligned viral genomes. Our method does not insist on conserved gene structure between the two sequences, thus making it applicable for the pairwise comparison of more distantly related sequences. Results...... and HIV2, as well as of two different Hepatitis Viruses, attaining results of ~87% sensitivity and ~98.5% specificity. We subsequently incorporate prior knowledge by "knowing" the gene structure of one sequence and annotating the other conditional on it. Boosting accuracy close to perfect we demonstrate...

  17. A Measurement of $R_b$ using Mutually Exclusive Tags

    Barate, R; Décamp, D; Ghez, P; Goy, C; Lees, J P; Lucotte, A; Minard, M N; Nief, J Y; Pietrzyk, B; Casado, M P; Chmeissani, M; Comas, P; Crespo, J M; Delfino, M C; Fernández, E; Fernández-Bosman, M; Garrido, L; Juste, A; Martínez, M; Miquel, R; Mir, L M; Orteu, S; Padilla, C; Park, I C; Pascual, A; Perlas, J A; Riu, I; Sánchez, F; Teubert, F; Colaleo, A; Creanza, D; De Palma, M; Gelao, G; Iaselli, Giuseppe; Maggi, G; Maggi, M; Marinelli, N; Nuzzo, S; Ranieri, A; Raso, G; Ruggieri, F; Selvaggi, G; Silvestris, L; Tempesta, P; Tricomi, A; Zito, G; Huang, X; Lin, J; Ouyang, Q; Wang, T; Xie, Y; Xu, R; Xue, S; Zhang, J; Zhang, L; Zhao, W; Abbaneo, D; Alemany, R; Becker, U; Bazarko, A O; Bright-Thomas, P G; Cattaneo, M; Cerutti, F; Drevermann, H; Forty, Roger W; Frank, M; Hagelberg, R; Harvey, J; Janot, P; Jost, B; Kneringer, E; Knobloch, J; Lehraus, Ivan; Lutters, G; Mato, P; Minten, Adolf G; Moneta, L; Pacheco, A; Pusztaszeri, J F; Ranjard, F; Rensing, P E; Rizzo, G; Rolandi, Luigi; Schlatter, W D; Schmitt, M; Schneider, O; Tejessy, W; Tomalin, I R; Wachsmuth, H W; Wagner, A; Ajaltouni, Ziad J; Barrès, A; Boyer, C; Falvard, A; Ferdi, C; Gay, P; Guicheney, C; Henrard, P; Jousset, J; Michel, B; Monteil, S; Montret, J C; Pallin, D; Perret, P; Podlyski, F; Proriol, J; Rosnet, P; Rossignol, J M; Fearnley, Tom; Hansen, J B; Hansen, J D; Hansen, J R; Hansen, P H; Nilsson, B S; Rensch, B; Wäänänen, A; Daskalakis, G; Kyriakis, A; Markou, C; Simopoulou, Errietta; Siotis, I; Vayaki, Anna; Blondel, A; Bonneaud, G R; Brient, J C; Bourdon, P; Rougé, A; Rumpf, M; Valassi, Andrea; Verderi, M; Videau, H L; Candlin, D J; Parsons, M I; Focardi, E; Parrini, G; Zachariadou, K; Corden, M; Georgiopoulos, C H; Jaffe, D E; Antonelli, A; Bencivenni, G; Bologna, G; Bossi, F; Campana, P; Capon, G; Casper, David William; Chiarella, V; Felici, G; Laurelli, P; Mannocchi, G; Murtas, F; Murtas, G P; Passalacqua, L; Pepé-Altarelli, M; Curtis, L; Dorris, S J; Halley, A W; Knowles, I G; Lynch, J G; O'Shea, V; Raine, C; Scarr, J M; Smith, K; Teixeira-Dias, P; Thompson, A S; Thomson, E; Thomson, F; Turnbull, R M; Geweniger, C; Graefe, G; Hanke, P; Hansper, G; Hepp, V; Kluge, E E; Putzer, A; Schmidt, M; Sommer, J; Tittel, K; Werner, S; Wunsch, M; Beuselinck, R; Binnie, David M; Cameron, W; Dornan, Peter J; Girone, M; Goodsir, S M; Martin, E B; Moutoussi, A; Nash, J; Sedgbeer, J K; Stacey, A M; Williams, M D; Dissertori, G; Ghete, V M; Girtler, P; Kuhn, D; Rudolph, G; Betteridge, A P; Bowdery, C K; Colrain, P; Crawford, G; Finch, A J; Foster, F; Hughes, G; Sloan, Terence; Williams, M I; Galla, A; Giehl, I; Greene, A M; Hoffmann, C; Jakobs, K; Kleinknecht, K; Quast, G; Renk, B; Rohne, E; Sander, H G; Van Gemmeren, P; Zeitnitz, C; Aubert, Jean-Jacques; Benchouk, C; Bonissent, A; Bujosa, G; Calvet, D; Carr, J; Coyle, P; Diaconu, C A; Etienne, F; Konstantinidis, N P; Leroy, O; Motsch, F; Payre, P; Rousseau, D; Talby, M; Sadouki, A; Thulasidas, M; Trabelsi, K; Aleppo, M; Ragusa, F; Berlich, R; Blum, Walter; Brown, D; Büscher, V; Dietl, H; Dydak, Friedrich; Ganis, G; Gotzhein, C; Kroha, H; Lütjens, G; Lutz, Gerhard; Männer, W; Moser, H G; Richter, R H; Rosado-Schlosser, A; Schael, S; Settles, Ronald; Seywerd, H C J; Saint-Denis, R; Stenzel, H; Wiedenmann, W; Wolf, G; Boucrot, J; Callot, O; Chen, S; Choi, Y; Cordier, A; Davier, M; Duflot, L; Grivaz, J F; Heusse, P; Höcker, A; Jacholkowska, A; Jacquet, M; Kim, D W; Le Diberder, F R; Lefrançois, J; Lutz, A M; Nikolic, I A; Schune, M H; Simion, S; Tournefier, E; Veillet, J J; Videau, I; Zerwas, D; Azzurri, P; Bagliesi, G; Batignani, G; Bettarini, S; Bozzi, C; Calderini, G; Carpinelli, M; Ciocci, M A; Ciulli, V; Dell'Orso, R; Fantechi, R; Ferrante, I; Foà, L; Forti, F; Giassi, A; Giorgi, M A; Gregorio, A; Ligabue, F; Lusiani, A; Marrocchesi, P S; Messineo, A; Palla, Fabrizio; Sanguinetti, G; Sciabà, A; Spagnolo, P; Steinberger, Jack; Tenchini, Roberto; Tonelli, G; Vannini, C; Venturi, A; Verdini, P G; Blair, G A; Bryant, L M; Chambers, J T; Gao, Y; Green, M G; Medcalf, T; Perrodo, P; Strong, J A; Von Wimmersperg-Töller, J H; Botterill, David R; Clifft, R W; Edgecock, T R; Haywood, S; Maley, P; Norton, P R; Thompson, J C; Wright, A E; Bloch-Devaux, B; Colas, P; Emery, S; Kozanecki, Witold; Lançon, E; Lemaire, M C; Locci, E; Pérez, P; Rander, J; Renardy, J F; Roussarie, A; Schuller, J P; Schwindling, J; Trabelsi, A; Vallage, B; Black, S N; Dann, J H; Johnson, R P; Kim, H Y; Litke, A M; McNeil, M A; Taylor, G; Booth, C N; Boswell, R; Brew, C A J; Cartwright, S L; Combley, F; Kelly, M S; Lehto, M H; Newton, W M; Reeve, J; Thompson, L F; Böhrer, A; Brandt, S; Cowan, G D; Grupen, Claus; Saraiva, P; Smolik, L; Stephan, F; Apollonio, M; Bosisio, L; Della Marina, R; Giannini, G; Gobbo, B; Musolino, G; Rothberg, J E; Wasserbaech, S R; Armstrong, S R; Charles, E; Elmer, P; Ferguson, D P S; Gao, Y S; González, S; Greening, T C; Hayes, O J; Hu, H; Jin, S; McNamara, P A; Nachtman, J M; Nielsen, J; Orejudos, W; Pan, Y B; Saadi, Y; Scott, I J; Walsh, J; Wu Sau Lan; Wu, X; Yamartino, J M; Zobernig, G


    A measurement of $R_b$ using five mutually exclusive hemisphere tags has been pe rformed by ALEPH using the full LEP1 statistics. Three tags are designed to sele ct the decay of the $Z^0$ to $b$ quarks, while the remaining two select $Z^0$ decays to $c$ and light quarks, and are used to measure the tagging efficiencies. The result, {$R_b~=~0.2159~\\pm~0.0009\\mbox{(stat)}~\\pm 0.0011\\mbox{(syst)}$}, is in agreement with the electroweak theory prediction of $0.2158 \\pm 0.0003$.

  18. Measurement of $R_{b}$ using a Vertex Mass Tag

    Abe, K; Akagi, T; Allen, N J; Ash, W W; Aston, D; Baird, K G; Baltay, C; Band, H R; Barakat, M B; Baranko, G; Bardon, O; Barklow, T L; Bashindzhagian, G L; Bazarko, A O; Ben-David, R; Benvenuti, Alberto C; Bilei, G M; Bisello, D; Blaylock, G; Bogart, J R; Bolen, B; Bolton, T; Bower, G R; Brau, J E; Breidenbach, M; Bugg, W M; Burke, D; Burnett, T H; Burrows, P N; Busza, W; Calcaterra, A; Caldwell, D O; Calloway, D; Camanzi, B; Carpinelli, M; Cassell, R; Castaldi, R; Castro, A; Cavalli-Sforza, M; Chou, A; Church, E; Cohn, H O; Coller, J A; Cook, V; Cotton, R; Cowan, R F; Coyne, D G; Crawford, G; de Oliveira, A; Damerell, C J S; Daoudi, M; De Groot, N; De Sangro, R; Dell'Orso, R; Dervan, P J; Dima, M; Dong, D N; Du, P Y C; Dubois, R; Eisenstein, B I; Elia, R; Etzion, E; Fahey, S; Falciai, D; Fan, C; Fernández, J P; Fero, M J; Frey, R; Gillman, T; Gladding, G; González, S; Hart, E L; Harton, J L; Hasan, A; Hasegawa, Y; Hasuko, K; Hedges, S J; Hertzbach, S S; Hildreth, M D; Huber, J; Huffer, M E; Hughes, E W; Hwang, H; Iwasaki, Y; Jackson, D J; Jacques, P; Jaros, J A; Jiang, Z Y; Johnson, A S; Johnson, J R; Johnson, R A; Junk, T R; Kajikawa, R; Kalelkar, M; Kang, H J; Karliner, I; Kawahara, H; Kendall, H W; Kim, Y D; King, M E; King, R; Kofler, R R; Krishna, N M; Kroeger, R S; Labs, J F; Langston, M; Lath, A; Lauber, J A; Leith, D W G S; Lia, V; Liu, M X; Liu, X; Loreti, M; Lu, A; Lynch, H L; Ma, J; Mancinelli, G; Manly, S; Mantovani, G C; Markiewicz, T W; Maruyama, T; Masuda, H; Mazzucato, E; McKemey, A K; Meadows, B T; Messner, R; Mockett, P M; Moffeit, K C; Moore, T B; Müller, D; Nagamine, T; Narita, S; Nauenberg, U; Neal, H; Nussbaum, M; Ohnishi, Y; Oishi, N; Onoprienko, D; Osborne, L S; Panvini, R S; Park, C H; Park, H; Pavel, T J; Peruzzi, I; Piccolo, M; Piemontese, L; Pieroni, E; Pitts, K T; Plano, R J; Prepost, R; Prescott, C Y; Punkar, G D; Quigley, J; Ratcliff, B N; Reeves, T W; Reidy, J; Reinertsen, P L; Rensing, P E; Rochester, L S; Rowson, P C; Russell, J J; Saxton, O H; Schalk, T; Schindler, R H; Schumm, B A; Schwiening, J; Sen, S; Serbo, V V; Shaevitz, M H; Shank, J T; Shapiro, G; Sherden, D J; Shmakov, K D; Simopoulos, C; Sinev, N B; Smith, S R; Smy, M B; Snyder, J A; Stängle, H; Stamer, P; Steiner, H; Steiner, R; Strauss, M G; Su, D; Suekane, F; Sugiyama, A; Suzuki, S; Swartz, M; Szumilo, A; Takahashi, T; Taylor, F E; Torrence, E; Trandafir, A I; Turk, J D; Usher, T; Vavra, J; Vannini, C; Vella, E; Venuti, J P; Verdier, R; Verdini, P G; Wagner, D L; Wagner, S R; Waite, A P; Watts, S J; Weidemann, A W; Weiss, E R; Whitaker, J S; White, S L; Wickens, F J; Williams, D C; Williams, S H; Willocq, S; Wilson, R J; Wisniewski, W J; Woods, M; Word, G B; Wyss, J; Yamamoto, R K; Yamartino, J M; Yang, X; Yashima, J; Yellin, S J; Young, C C; Yuta, H; Zapalac, G; Zdarko, R W; Zhou, J


    We report a new measurement of Rb = Gamma(Z0->b-bbar) / Gamma(Z0->hadrons) using a double tag technique, where the b hemisphere selection is based on the reconstructed mass of the B hadron decay vertex. The measurement was performed using a sample of 130k hadronic Z0 events, collected with the SLD at the SLC. The method utilizes the 3-D vertexing abilities of the CCD pixel vertex detector and the small stable SLC beams to obtain a high b-tagging efficiency and purity. We obtain Rb=0.2142+/-0.0034(stat.)+/-0.0015(syst.)+/-0.0002(R_c).

  19. Structure and chromosomal localization of the gene encoding the human myelin protein zero (MPZ)

    Hayasaka, Kiyoshi; Himoro, Masato; Takada, Goro (Akita Univ. School of Medicine, Akita (Japan)); Wang, Yimin; Takata, Mizuho; Minoshima, Shinsei; Shimizu, Nobuyoshi; Miura, Masayuki; Uyemura, Keiichi (Keio Univ. School of Medicine, Tokyo (Japan))


    The authors describe the cloning, characterization, and chromosomal mapping of the human myelin protein zero (MPZ) gene (a structural protein of myelin and an adhesive glycoprotein of the immunoglobulin superfamily). The gene is about 7 kb long and consists of six exons corresponding of the functional domains. All exon-intron junction sequences conform to the GT/AG rule. The 5[prime]-flanking region of the gene has a TA-rich element (TATA-like box), two CAAT boxes, and a single defined transcription initiation site detected by the primer extension method. The gene for human MPZ was assigned to chromosome 1q22-q23 by spot blot hybridization of flow-sorted human chromosomes and fluorescence in situ hybridization. The localization of the MPZ gene coincides with the locus for Charcot-Marie-Tooth disease type 1B, determined by linkage analysis. 20 refs., 3 figs., 1 tab.

  20. Intron phase correlations and the evolution of the intron/exon structure of genes.

    Long, M; Rosenberg, C; Gilbert, W


    Two issues in the evolution of the intron/exon structure of genes are the role of exon shuffling and the origin of introns. Using a large data base of eukaryotic intron-containing genes, we have found that there are correlations between intron phases leading to an excess of symmetric exons and symmetric exon sets. We interpret these excesses as manifestations of exon shuffling and make a conservative estimate that at least 19% of the exons in the data base were involved in exon shuffling, suggesting an important role for exon shuffling in evolution. Furthermore, these excesses of symmetric exons appear also in those regions of eukaryotic genes that are homologous to prokaryotic genes: the ancient conserved regions. This last fact cannot be explained in terms of the insertional theory of introns but rather supports the concept that some of the introns were ancient, the exon theory of genes. PMID:8618928

  1. Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.

    Xiaodong Cai

    Full Text Available Integrating genetic perturbations with gene expression data not only improves accuracy of regulatory network topology inference, but also enables learning of causal regulatory relations between genes. Although a number of methods have been developed to integrate both types of data, the desiderata of efficient and powerful algorithms still remains. In this paper, sparse structural equation models (SEMs are employed to integrate both gene expression data and cis-expression quantitative trait loci (cis-eQTL, for modeling gene regulatory networks in accordance with biological evidence about genes regulating or being regulated by a small number of genes. A systematic inference method named sparsity-aware maximum likelihood (SML is developed for SEM estimation. Using simulated directed acyclic or cyclic networks, the SML performance is compared with that of two state-of-the-art algorithms: the adaptive Lasso (AL based scheme, and the QTL-directed dependency graph (QDG method. Computer simulations demonstrate that the novel SML algorithm offers significantly better performance than the AL-based and QDG algorithms across all sample sizes from 100 to 1,000, in terms of detection power and false discovery rate, in all the cases tested that include acyclic or cyclic networks of 10, 30 and 300 genes. The SML method is further applied to infer a network of 39 human genes that are related to the immune function and are chosen to have a reliable eQTL per gene. The resulting network consists of 9 genes and 13 edges. Most of the edges represent interactions reasonably expected from experimental evidence, while the remaining may just indicate the emergence of new interactions. The sparse SEM and efficient SML algorithm provide an effective means of exploiting both gene expression and perturbation data to infer gene regulatory networks. An open-source computer program implementing the SML algorithm is freely available upon request.

  2. Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification.

    Ohyama, K; Fukuzawa, H; Kohchi, T; Sano, T; Sano, S; Shirai, H; Umesono, K; Shiki, Y; Takeuchi, M; Chang, Z


    We have determined the complete nucleotide sequence of chloroplast DNA from a liverwort, Marchantia polymorpha, using a clone bank of chloroplast DNA fragments. The circular genome consists of 121,024 base-pairs and includes two large inverted repeats (IRA and IRB, each 10,058 base-pairs), a large single-copy region (LSC, 81,095 base-pairs), and a small single-copy region (SSC, 19,813 base-pairs). The nucleotide sequence was analysed with a computer to deduce the entire gene organization, assuming the universal genetic code and the presence of introns in the coding sequences. We detected 136 possible genes. 103 gene products of which are related to known stable RNA or protein molecules. Stable RNA genes for four species of ribosomal RNA and 32 species of tRNA were located, although one of the tRNA genes may be defective. Twenty genes encoding polypeptides involved in photosynthesis and electron transport were identified by comparison with known chloroplast genes. Twenty-five open reading frames (ORFs) show structural similarities to Escherichia coli RNA polymerase subunits, 19 ribosomal proteins and two related proteins. Seven ORFs are comparable with human mitochondrial NADH dehydrogenase genes. A computer-aided homology search predicted possible chloroplast homologues of bacterial proteins; two ORFs for bacterial 4Fe-4S-type ferredoxin, two for distinct subunits of a protein-dependent transport system, one ORF for a component of nitrogenase, and one for an antenna protein of a light-harvesting complex. The other 33 ORFs, consisting of 29 to 2136 codons, remain to be identified, but some of them seem to be conserved in evolution. Detailed information on gene identification is presented in the accompanying papers. We postulated that there were 22 introns in 20 genes (8 tRNA genes and 12 ORFs), which may be classified into the groups I and II found in fungal mitochondrial genes. The structural gene for ribosomal protein S12 is trans-split on the opposite DNA strand

  3. The genomic structure of the human Charcot-Leyden crystal protein gene is analogous to those of the galectin genes

    Dyer, K.D. [National Inst. of Health, Bethesda, MD (United States)]|[Georgetown Univ. Medical Center, Washington, DC (United States); Handen, J.S.; Rosenberg, H.F. [National Inst. of Health, Bethesda, MD (United States)


    The Charcot-Leyden crystal (CLC) protein, or eosinophil lysophospholipase, is a characteristic protein of human eosinophils and basophils; recent work has demonstrated that the CLC protein is both structurally and functionally related to the galectin family of {beta}-galactoside binding proteins. The galectins as a group share a number of features in common, including a linear ligand binding site encoded on a single exon. In this work, we demonstrate that the intron-exon structure of the gene encoding CLC is analogous to those encoding the galectins. The coding sequence of the CLC gene is divided into four exons, with the entire {beta}-galactoside binding site encoded by exon III. We have isolated CLC {beta}-galactoside binding sites from both orangutan (Pongo pygmaeus) and murine (Mus musculus) genomic DNAs, both encoded on single exons, and noted conservation of the amino acids shown to interact directly with the {beta}-galactoside ligand. The most likely interpretation of these results suggests the occurrence of one or more exon duplication and insertion events, resulting in the distribution of this lectin domain to CLC as well as to the multiple galectin genes. 35 refs., 3 figs.

  4. Robustness and state-space structure of Boolean gene regulatory models.

    Willadsen, Kai; Wiles, Janet


    Robustness to perturbation is an important characteristic of genetic regulatory systems, but the relationship between robustness and model dynamics has not been clearly quantified. We propose a method for quantifying both robustness and dynamics in terms of state-space structures, for Boolean models of genetic regulatory systems. By investigating existing models of the Drosophila melanogaster segment polarity network and the Saccharomyces cerevisiae cell-cycle network, we show that the structure of attractor basins can yield insight into the underlying decision making required of the system, and also the way in which the system maximises its robustness. In particular, gene networks implementing decisions based on a few genes have simple state-space structures, and their attractors are robust by virtue of their simplicity. Gene networks with decisions that involve many interacting genes have correspondingly more complicated state-space structures, and robustness cannot be achieved through the structure of the attractor basins, but is achieved by larger attractor basins that dominate the state space. These different types of robustness are demonstrated by the two models: the D. melanogaster segment polarity network is robust due to simple attractor basins that implement decisions based on spatial signals; the S. cerevisiae cell-cycle network has a complicated state-space structure, and is robust only due to a giant attractor basin that dominates the state space.

  5. A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data.

    Gui, Shupeng; Rice, Andrew P; Chen, Rui; Wu, Liang; Liu, Ji; Miao, Hongyu


    Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. Moreover, recent work suggests that these methods still suffer from the curse of dimensionality if a network size increases to 100 or higher. Here we present a novel scalable algorithm for identifying genome-wide gene regulatory network (GRN) structures, and we have verified the algorithm performances by extensive simulation studies based on the DREAM challenge benchmark data. The highlight of our method is that its superior performance does not degenerate even for a network size on the order of 10(4), and is thus readily applicable to large-scale complex networks. Such a breakthrough is achieved by considering both prior biological knowledge and multiple topological properties (i.e., sparsity and hub gene structure) of complex networks in the regularized formulation. We also validate and illustrate the application of our algorithm in practice using the time-course gene expression data from a study on human respiratory epithelial cells in response to influenza A virus (IAV) infection, as well as the CHIP-seq data from ENCODE on transcription factor (TF) and target gene interactions. An interesting finding, owing to the proposed algorithm, is that the biggest hub structures (e.g., top ten) in the GRN all center at some transcription factors in the context of epithelial cell infection by IAV. The proposed algorithm is the first scalable method for large complex network structure identification. The GRN structure identified by our algorithm could reveal possible biological links and help researchers to choose which gene functions to investigate in a biological event. The algorithm described in this article is implemented in MATLAB (Ⓡ) , and the source code is

  6. Biotransformation of ginsenoside Rb1 to ginsenoside C-K by endophytic fungus Arthrinium sp. GE 17-18 isolated from Panax ginseng.

    Fu, Y; Yin, Z-H; Wu, L-P; Yin, C-R


    This research aimed to isolate β-glycosidase-producing endophytic fungus in Panax ginseng to achieve biotransformation of ginsenoside Rb1 to ginsenoside C-K. Of these 15 β-glucosidase-producing endophytic fungus isolated from ginseng roots, a β-glucosidase-producing endophytic fungi GE 17-18 could hydrolyse major ginsenosides Rb1 to minor ginsenoside C-K with metabolic pathways: ginsenoside Rb1→ginsenoside Rd→ginsenoside F2→ginsenoside C-K. Phylogenetic analysis of ITS gene sequences indicated that the strain GE 17-18 belongs to the genus Arthrinium and is most closely related to Arthrinium sp. HQ832803.1. This is the first study to provide information of cultivable β-glycosidase-producing Endophytic fungus in Panax ginseng. The strain GE 17-18 has potential to be applied on the preparation for minor ginsenoside C-K in pharmaceutical industry. © 2016 The Society for Applied Microbiology.

  7. Regulation of genes involved in cell wall synthesis and structure during Ustilago maydis dimorphism.

    Robledo-Briones, Mariana; Ruiz-Herrera, José


    The cell wall is the structure that provides the shape to fungal cells and protects them from the difference in osmotic pressure existing between the cytosol and the external medium. Accordingly, changes in structure and composition of the fungal wall must occur during cell differentiation, including the dimorphic transition of fungi. We analyzed, by use of microarrays, the transcriptional regulation of the 639 genes identified to be involved in cell wall synthesis and structure plus the secretome of the Basidiomycota species Ustilago maydis during its dimorphic transition induced by a change in pH. Of these, 189 were differentially expressed during the process, and using as control two monomorphic mutants, one yeast like and the other mycelium constitutive, 66 genes specific of dimorphism were identified. Most of these genes were up-regulated in the mycelial phase. These included CHS genes, genes involved in β-1,6-glucan synthesis, N-glycosylation, and proteins containing a residue of glycosylphosphatidylinositol, and a number of genes from the secretome. The possible significance of these data on cell wall plasticity is discussed.

  8. [Cloning and structure analysis of zinc finger protein gene in Populus euphratica Oliv].

    Wang, Jun-Ying; Yin, Wei-Lun; Xia, Xin-Li


    Zinc finger proteins belong to a family of nuclear transcription factors which function is to regulate gene expression in both prokaryotic and eukaryotic cells. A pair of primers was designed after analyzing the conservation of salt-tolerant zinc protein Alfin-1 in such diverse plants as alfalfa and Arabidopsis. The zinc finger protein gene is isolated from total RNA with RT-PCR in aquaculture leaves of Populus euphratica . Its full cDNA length is 924bp. Analysis of its amino acid sequence showed it has a typical Cys(2)/His(2) zinc finger structure and a G-rich promoter binding site GTGGGG, starting from position 556. Since transcrptional factors which have the same function show conservation in structure and amino acid sequence of DNA binding region, the structure analysis in this paper indicates the cloned zinc finger protein gene may have functional correlation to Alfin-1.

  9. A framework for scalable parameter estimation of gene circuit models using structural information

    Kuwahara, Hiroyuki


    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  10. Menzerath-Altmann law in mammalian exons reflects the dynamics of gene structure evolution.

    Nikolaou, Christoforos


    Genomic sequences exhibit self-organization properties at various hierarchical levels. One such is the gene structure of higher eukaryotes with its complex exon/intron arrangement. Exon sizes and exon numbers in genes have been shown to conform to a law derived from statistical linguistics and formulated by Menzerath and Altmann, according to which the mean size of the constituents of an entity is inversely related to the number of these constituents. We herein perform a detailed analysis of this property in the complete exon set of the mouse genome in correlation to the sequence conservation of each exon and the transcriptional complexity of each gene locus. We show that extensive linear fits, representative of accordance to Menzerath-Altmann law are restricted to a particular subset of genes that are formed by exons under low or intermediate sequence constraints and have a small number of alternative transcripts. Based on this observation we propose a hypothesis for the law of Menzerath-Altmann in mammalian genes being predominantly due to genes that are more versatile in function and thus, more prone to undergo changes in their structure. To this end we demonstrate one test case where gene categories of different functionality also show differences in the extent of conformity to Menzerath-Altmann law. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Molecular ions in ultracold atomic gases: computed electronic interactions for \\MgHion with Rb

    Tacconi, Mario


    The electronic structures of the manifold of potential energy surfaces generated in the lower energy range by the interaction of the MgH$^+$(X$^1\\Sigma^+$) cationic molecule with Rb($^2$S), neutral atom are obtained over a broad range of Jacobi coordinates from strongly correlated \\emph{ab initio} calculations which use a Multireference (MR) wavefunction within a Complete Active Space (CAS) approach. The relative features of the lowest five surfaces are analyzed in terms of possible collisional outcomes when employed to model the ultracold dynamics of ionic molecular partners.

  12. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block

    Ma Wujun


    Full Text Available Abstract Background The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and

  13. Cyclin-dependent kinase-mediated phosphorylation of RBP1 and pRb promotes their dissociation to mediate release of the SAP30·mSin3·HDAC transcriptional repressor complex.

    Suryadinata, Randy; Sadowski, Martin; Steel, Rohan; Sarcevic, Boris


    Eukaryotic cell cycle progression is mediated by phosphorylation of protein substrates by cyclin-dependent kinases (CDKs). A critical substrate of CDKs is the product of the retinoblastoma tumor suppressor gene, pRb, which inhibits G(1)-S phase cell cycle progression by binding and repressing E2F transcription factors. CDK-mediated phosphorylation of pRb alleviates this inhibitory effect to promote G(1)-S phase cell cycle progression. pRb represses transcription by binding to the E2F transactivation domain and recruiting the mSin3·histone deacetylase (HDAC) transcriptional repressor complex via the retinoblastoma-binding protein 1 (RBP1). RBP1 binds to the pocket region of pRb via an LXCXE motif and to the SAP30 subunit of the mSin3·HDAC complex and, thus, acts as a bridging protein in this multisubunit complex. In the present study we identified RBP1 as a novel CDK substrate. RBP1 is phosphorylated by CDK2 on serines 864 and 1007, which are N- and C-terminal to the LXCXE motif, respectively. CDK2-mediated phosphorylation of RBP1 or pRb destabilizes their interaction in vitro, with concurrent phosphorylation of both proteins leading to their dissociation. Consistent with these findings, RBP1 phosphorylation is increased during progression from G(1) into S-phase, with a concurrent decrease in its association with pRb in MCF-7 breast cancer cells. These studies provide new mechanistic insights into CDK-mediated regulation of the pRb tumor suppressor during cell cycle progression, demonstrating that CDK-mediated phosphorylation of both RBP1 and pRb induces their dissociation to mediate release of the mSin3·HDAC transcriptional repressor complex from pRb to alleviate transcriptional repression of E2F.

  14. Certificate Revocation System's Based on RB_Tree%基于RB_Tree的证书吊销系统



    提出了公钥基础设施(Public Key Infrastructure,PKI)中证书吊销问题的一种解决方案--RB_搜索树解决方案(Certificate Revocation RB_Tree,CRRBT).该方案在查询与更新时最大时间复杂度始终保持在O(log2n)量级,对工程实现具有一定的指导意义.

  15. Supramolecular Aggregate as a High-Efficiency Gene Carrier Mediated with Optimized Assembly Structure.

    Zhang, Yi; Duan, Junkun; Cai, Lingguang; Ma, Dong; Xue, Wei


    For cancer gene therapy, a safe and high-efficient gene carrier is a must. To resolve the contradiction between gene transfection efficiency and cytotoxicity, many polymers with complex topological structures have been synthesized, although their synthesis processes and structure control are difficult as well as the high molecular weight also bring high cytotoxicity. We proposed an alternative strategy that uses supramolecular inclusion to construct the aggregate from the small molecules for gene delivery, and to further explore the relationship between the topological assembly structure and their ability to deliver gene. Herein, PEI-1.8k-conjugating β-CD through 6-hydroxyl (PEI-6-CD) and 2-hydroxyl (PEI-2-CD) have been synthesized respectively and then assembled with diferrocene (Fc)-ended polyethylene glycol (PEG-Fc). The obtained aggregates were then used to deliver MMP-9 shRNA plasmid for MCF-7 cancer therapy. It was found that the higher gene transfection efficiency can be obtained by selecting PEI-2-CD as the host and tuning the host/guest molar ratios. With the rational modulation of supramolecular architectures, the aggregate played the functions similar to macromolecules which exhibit higher transfection efficiency than PEI-25k, but show much lower cytotoxicity because of the nature of small/low molecules. In vitro and in vivo assays confirmed that the aggregate could deliver MMP-9 shRNA plasmid effectively into MCF-7 cells and then downregulate MMP-9 expression, which induced the significant MCF-7 cell apoptosis, as well inhibit MCF-7 tumor growth with low toxicity. The supramolecular aggregates maybe become a promising carrier for cancer gene therapy and also provided an alternative strategy for designing new gene carriers.

  16. Mitotic defects lead to pervasive aneuploidy and accompany loss of RB1 activity in mouse LmnaDhe dermal fibroblasts.

    C Herbert Pratt

    Full Text Available BACKGROUND: Lamin A (LMNA is a component of the nuclear lamina and is mutated in several human diseases, including Emery-Dreifuss muscular dystrophy (EDMD; OMIM ID# 181350 and the premature aging syndrome Hutchinson-Gilford progeria syndrome (HGPS; OMIM ID# 176670. Cells from progeria patients exhibit cell cycle defects in both interphase and mitosis. Mouse models with loss of LMNA function have reduced Retinoblastoma protein (RB1 activity, leading to aberrant cell cycle control in interphase, but how mitosis is affected by LMNA is not well understood. RESULTS: We examined the cell cycle and structural phenotypes of cells from mice with the Lmna allele, Disheveled hair and ears (Lmna(Dhe. We found that dermal fibroblasts from heterozygous Lmna(Dhe (Lmna(Dhe/+ mice exhibit many phenotypes of human laminopathy cells. These include severe perturbations to the nuclear shape and lamina, increased DNA damage, and slow growth rates due to mitotic delay. Interestingly, Lmna(Dhe/+ fibroblasts also had reduced levels of hypophosphorylated RB1 and the non-SMC condensin II-subunit D3 (NCAP-D3, a mitosis specific centromere condensin subunit that depends on RB1 activity. Mitotic check point control by mitotic arrest deficient-like 1 (MAD2L1 also was perturbed in Lmna(Dhe/+ cells. Lmna(Dhe/+ fibroblasts were consistently aneuploid and had higher levels of micronuclei and anaphase bridges than normal fibroblasts, consistent with chromosome segregation defects. CONCLUSIONS: These data indicate that RB1 may be a key regulator of cellular phenotype in laminopathy-related cells, and suggest that the effects of LMNA on RB1 include both interphase and mitotic cell cycle control.

  17. Association analysis of p16 (CDKN2A) and RB1 polymorphisms with susceptibility to cervical cancer in Indian population.

    Thakur, Nisha; Hussain, Showket; Nasare, Vilas; Das, Bhudev C; Basir, Seemi Farhat; Bharadwaj, Mausumi


    The potent tumor suppressors P16 and RB1 are the key regulators of cell cycle machinery in eukaryotes. Polymorphisms in these genes play an important role in the outcome of various diseases including cancer. In the present study, we evaluated the association of p16 and RB1 polymorphisms with cervical cancer susceptibility in Indian population. We screened 150 histologically confirmed cervical cancer cases along with equal number of healthy controls with normal cervical cytology. PCR-RFLP method was employed for genotyping of SNPs in p16 C540G (rs11515), C580T (rs3088440) in the 3'-UTR of exon 3 and RB1 A153104G (rs4151580) located in the intron 18 and confirmed by direct sequencing. Both patients and controls were screened for HPV infection. In this case-control study 84.67% (127/150) of cases were found to be positive for HPV DNA sequence. Women carrying p16 C540G carrier genotypes 540 (CG/GG) may have protective effect for the development of cervical cancer (P=0.0001, OR=0.31, 95% CI=0.17-0.56). And SNP at C580T of p16 gene was found to be negatively associated with the risk of cervical cancer (P=0.0004, OR=0.04, 95% CI=0.002-0.63). p16 (540C/580T) has emerged as a major risk haplotype (P=0.033, OR=1.47, 95% CI=1.05-2.07) whereas p16 (540G/580T) as a chief protective haplotype (P=0.014, OR=0.39, 95% CI=0.18-0.83) for the development of cervical cancer among Indian women. Contrary to this, SNP at A153104G of RB1 gene showed statistically significant association (P=0.035, OR=1.69, 95% CI=1.06-2.68) with increased susceptibility for the development of cervical cancer. Our results suggest that single nucleotide polymorphisms in p16, RB1 genes may affect the susceptibility to cervical cancer collectively.

  18. Genetic and bibliographic information: IL10RB [GenLibi

    Full Text Available IL10RB interleukin 10 receptor, beta human Periodontitis (MeSH) Stomatognathic Dise...ases (C07) > Mouth Diseases (C07.465) > Periodontal Diseases (C07.465.714) > Periodontitis (C07.465.714.533) 02A0614091 ...

  19. Mass measurements of neutron-rich Rb and Sr isotopes

    Klawitter, R; Brodeur, M; Chowdhury, U; Chausdhuri, A; Fallis, J; Gallant, A T; Grossheim, A; Kwiatkowski, A A; Lascar, D; Leach, K G; Lennarz, A; Macdonald, T D; Pearkes, J; Seeraji, S; Simon, M C; Simon, V V; Schultz, B E; Dilling, J


    We report on the mass measurements of several neutron-rich $\\mathrm{Rb}$ and $\\mathrm{Sr}$ isotopes in the $A \\approx 100$ region with the TITAN Penning-trap mass spectrometer. Using highly charged ions in the charge state $q=10+$, the masses of $^{98,99}\\mathrm{Rb}$ and $^{98-100}\\mathrm{Sr}$ have been determined with a precision of $6 - 12\\ \\mathrm{keV}$, making their uncertainty negligible for r-process nucleosynthesis network calculations. The mass of $^{101}\\mathrm{Sr}$ has been determined directly for the first time with a precision eight times higher than the previous indirect measurement and a deviation of $3\\sigma$ when compared to the Atomic Mass Evaluation. We also confirm the mass of $^{100}\\mathrm{Rb}$ from a previous measurement. Furthermore, our data indicates the existance of a low-lying isomer with $80\\ \\mathrm{keV}$ excitation energy in $^{98}\\mathrm{Rb}$. We show that our updated mass values lead to minor changes in the r-process by calculating fractional abundances in the $A\\approx 100$ re...

  20. RB962962, a sugarcane cultivar for late harvest

    Luiz José Oliveira Tavares de Melo


    Full Text Available In the Northeast of Brazil, sugarcane cultivar RB962962 is harvested at the end of the cycle, between December and February, with a high sugar yield per area. Recommended for sandy soils of medium texture and fertility, it is resistant to the major diseases and fast-growing in plant and ratoon crops.

  1. Dissecting Pin1 and phospho-pRb regulation.

    Rizzolio, Flavio; Caligiuri, Isabella; Lucchetti, Chiara; Fratamico, Robert; Tomei, Valentina; Gallo, Gaia; Agelan, Alexis; Ferrari, Giovanni; Toffoli, Giuseppe; Klein-Szanto, Andres J; Giordano, Antonio


    The activity of the Retinoblastoma protein, the master regulator of the cell cycle, is finely regulated by phosphorylation. CDKs and cyclins are major players in phosphorylation and it has been recently discovered that the prolyl isomerase Pin1 is an essential protein that orchestrates this process. In this article, we report new findings regarding the role of Pin1 in the pRb pathway. Our data suggest that PI3K, CDKs, and the Pin1 axis have a critical role in sustaining the complete phosphorylation of pRb. Furthermore, we analyze the correlation between Pin1 and pRb phosphorylation in vivo. We show that, in human malignant glioma tissue microarrays (TMA) and in Pin1 knockout (KO) mice, there is a positive correlation between Pin1 and pRb phosphorylation. Prospectively, our findings suggest that the synergism between CDKs, Pin1, and PI3K inhibitors hold great promise for targeted pharmacological treatment of cancer patients, with the possibility of reaching high effectiveness at tolerated doses.

  2. A remotely interrogated all-optical Rb-87 magnetometer

    Patton, B.; Versolato, O. O.; Hovde, D. C.; Corsini, E.; Higbie, J. M.; Budker, D.


    Atomic magnetometry was performed at Earth's magnetic field over a free-space distance of ten meters. Two laser beams aimed at a distant alkali-vapor cell excited and detected the Rb-87 magnetic resonance, allowing the magnetic field within the cell to be interrogated remotely. Operated as a driven

  3. Collection of $^{83}$Rb at low implantation energy for KATRIN

    Zboril, M

    KATRIN, the KArlsruhe TRItium Neutrino experiment aims to measure the neutrino mass by spectroscopy of the tritium $\\beta$-decay at the endpoint by means of Magnetic Adiabatic Collimation combined with an Electrostatic filter (MAC-E filter). To monitor the HV-system of the KATRIN-setup, we would need one or two $^{83}$Rb sources roughly every half a year.

  4. Sarco(endoplasmic Reticulum Ca2+-ATPase-2 Gene: Structure and Transcriptional Regulation of the Human Gene

    Angel Zarain-Herzberg


    Full Text Available The sarco(endoplasmic reticulum Ca2+-ATPases (SERCAs belong to a family of active calcium transport enzymes encoded by the SERCA1, 2, and 3 genes. In this study, we describe the complete structure of the human SERCA2 gene and its 5’ -regulatory region. The hSERCA2 gene is located in chromosome 12 position q24.1 in Contig NT_009770.8, spans 70 kb, and is organized in 21 exons intervened by 20 introns. The last two exons of the pre-mRNA produce by alternatively splicing the cardiac/slow-twitch muscle-specific SERCA2a isoform and the ubiquitous SERCA2b isoform. The sequence of the proximal 225-bp regulatory region of the SERCA2 genes is 80% G+C-rich and is conserved among human, rabbit, rat, and mouse species. It contains a TATA-like-box, an E-box/USF sequence, a CAAT-box, four Sp1 binding sites, and a thyroid hormone responsive element (TRE. There are two other conserved regulatory regions located between positions -410 to -661 bp and from -919 to -1410 bp. Among the DNA cis-elements present in these two regulatory regions there are potential binding sites for: GATA-4, -5, -6, Nkx-2.5/Csx, OTF-1, USF, MEF-2, SRF, PPAR/RXR, AP-2, and TREs. Upstream from position -1.5 kb, there is no significant homology among the SERCA2 genes cloned. In addition, the human gene has several repeated sequences mainly of the Alu and L2 type located upstream from position -1.7 kb, spanning in a continuous fashion for more than 40 kb. In this study, we report the cloning of 2.4 kb of 5’-regulatory region and demonstrate that the proximal promoter region is sufficient for expression in cardiac myocytes, and the region from -225 to -1232 bp contains regulatory DNA elements which down-regulate the expression of the SERCA2 gene in neonatal cardiomyocytes.

  5. Frequent disruption of the RB1 pathway in diffuse large B cell lymphoma

    Møller, M B; Kania, Per Walter; Ino, Y


    In the present study, we analysed 34 de novo diffuse large B cell lymphoma (DLCL) from a population-based lymphoma registry for alterations of the RB1 pathway at the genetic (RB1 and CDK4) and protein (pRb, cyclin D1, cyclin D3, CDK4, and E2F-1) level. The results were correlated with the data fr...

  6. Expression of CD45RB functionally distinguishes intestinal T lymphocytes in inflammatory bowel disease.

    Hove, T. ten; The Olle, F.; Berkhout, M.; Bruggeman, J.P.; Vyth-Dreese, F.A.; Slors, J.F.M.; Deventer, S.J.H. van; Velde, A.A. te


    The importance of CD45RB expression on T cells was already shown in mice where CD45RB(high) expression determines pathogenic potential. In this study, we analyzed the expression of CD45RA, CD45RB, and CD45RO on CD4(+) T lymphocytes in the intestinal mucosa and in the circulation of patients with inf

  7. Treating cancer when pRb and p53 cannot be reactivated.

    Zhu, Liang


    Activation of oncoproteins and inactivation of tumor suppressors induces tumorigenesis. When these events happen upstream of pRb and p53, cancer therapies may initially succeed and then fail when pRb and p53 are activated and then re-inactivated. Therapies might succeed if they remain effective when pRb and p53 are genetically inactivated.

  8. Immune responses of bison and efficacy after booster vaccination with Brucella abortus strain RB51

    Thirty-one bison heifers were randomly assigned to saline (control; n=7) or single vaccination (n=24) with 1010 CFU of B. abortus strain RB51 (RB51). Some vaccinated bison were randomly selected for booster vaccination with 10**10 CFU of RB51 at 11 months after initial vaccination (n=16). When comp...

  9. Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

    T. A. Hughes


    Full Text Available Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

  10. Shifts in the ESR spectra of alkali-metal atoms (Li, Na, K, Rb) on helium nanodroplets.

    Hauser, Andreas W; Gruber, Thomas; Filatov, Michael; Ernst, Wolfgang E


    He-droplet-induced changes of the hyperfine structure constants of alkali-metal atoms are investigated by a combination of relativistically corrected ab initio methods with a simulation of the helium density distribution based on He density functional theory. Starting from an accurate description of the variation of the hyperfine structure constant in the M-He diatomic systems (M=Li, Na, K, Rb) as a function of the interatomic distance we simulate the shifts induced by droplets of up to 10,000 (4)He atoms. All theoretical predictions for the relative shifts in the isotropic hyperfine coupling constants of the alkali-metal atoms attached to helium droplets of different size are then tied to a single, experimentally derived parameter of Rb.

  11. Analysis of flavonoids and the flavonoid structural genes in brown fiber of upland cotton.

    Hongjie Feng

    Full Text Available BACKGROUND: As a result of changing consumer preferences, cotton (Gossypium Hirsutum L. from varieties with naturally colored fibers is becoming increasingly sought after in the textile industry. The molecular mechanisms leading to colored fiber development are still largely unknown, although it is expected that the color is derived from flavanoids. EXPERIMENTAL DESIGN: Firstly, four key genes of the flavonoid biosynthetic pathway in cotton (GhC4H, GhCHS, GhF3'H, and GhF3'5'H were cloned and studied their expression profiles during the development of brown- and white cotton fibers by QRT-PCR. And then, the concentrations of four components of the flavonoid biosynthetic pathway, naringenin, quercetin, kaempferol and myricetin in brown- and white fibers were analyzed at different developmental stages by HPLC. RESULT: The predicted proteins of the four flavonoid structural genes corresponding to these genes exhibit strong sequence similarity to their counterparts in various plant species. Transcript levels for all four genes were considerably higher in developing brown fibers than in white fibers from a near isogenic line (NIL. The contents of four flavonoids (naringenin, quercetin, kaempferol and myricetin were significantly higher in brown than in white fibers and corresponding to the biosynthetic gene expression levels. CONCLUSIONS: Flavonoid structural gene expression and flavonoid metabolism are important in the development of pigmentation in brown cotton fibers.

  12. Genetic regulation of tissue-specific expression of amylase structural genes in Drosophila melanogaster.

    Abraham, I; Doane, W W


    Laboratory strains of Drosophila melanogaster were screened for spatial variations in adult midgut alpha-amylase (1,4-alpha-D-glucan glucanohydrolase, EC expression. No strain-specific differences were found anteriorly, but three patterns of activity were discerned in the posterior midgut: A, activity throughout most of the region; B, activity in the anterior part of the region; and C, little or no activity. Alleles of a control gene, map, are responsible for this tissue-specific regulation of activity; e.g., mapA homozygotes produce the A pattern and mapC homozygotes the C pattern. The map locus was placed at 2--80 +/- on the genetic map of chromosome 2R, about two crossover units distal to the Amy structural gene region for alpha-amylase. Electrophoretic studies showed that mapA is trans acting in mapA/mapC flies, allowing expression of amylase isozymes coded for by genes on the opposite chromosome. The map gene behaves as a temporal gene that is clearly separable from the tightly linked, duplicated Amy structural genes. Images PMID:100784

  13. Structure and organization of the human thrombospondin 3 gene (THBS3)

    Adolph, K.W.; Long, G.L.; Bornstein, P. [Univ. of Washington, Seattle, WA (United States)] [and others


    The promoter/5{prime} flank sequence, cDNA sequence, and exon/intron structures of the human thrombospondin 3 (THBS3) gene have been determined. THBS3 cDNA clones were obtained by PCR amplification of human fetal lung cDNA using THBS3-specific primers. Analysis of cDNA and genomic sequences showed the THBS3 gene to be composed of 23 exons, 1 more than the number of exons in the previously characterized mouse TSP3 gene. The additional exon results from the division of mouse exon F into exons F1 and F2. The cDNA encodes a polypeptide of 956 amino acids that is highly acidic, with a clustering of acidic side chains in the third quarter of the polypeptide. This region corresponds to seven type III (Ca{sup 2+}-binding) repeats, a feature shared with other thrombospondins. In addition to these type III repeats, four type II (EGF-like) repeats and NH{sub 2}- and COOH-terminal domains are present in thrombospondin 3. The THBS3 and mouse TSP3 genes differ in intron sizes, but exon sequences and sizes and positions of insertion of introns are conserved to a high degree. The structural organization of the THBS3 gene is of interest because of its close proximity to that of metaxin, with which it shares a common promoter sequence, and to the gene encoding glucocerebrosidase, a deficiency in which causes Gaucher disease. 33 refs., 4 figs., 2 tabs.

  14. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Antoine Claessens


    Full Text Available The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1 that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs were scattered across the genome, structural variants (deletions, duplications, translocations were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7-72.4% yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

  15. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.

    Carlini, D B; Chen, Y; Stephan, W


    To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

  16. Review of accident analyses of RB experimental reactor

    Pešić Milan P.


    Full Text Available The RB reactor is a uranium fuel heavy water moderated critical assembly that has been put and kept in operation by the VTNCA Institute of Nuclear Sciences, Belgrade, Serbia and Montenegro, since April 1958. The first complete Safety Analysis Report of the RB reactor was prepared in 1961/62 yet, the first accident analysis had been made in late 1958 with the aim to examine a power transition and the total equivalent doses received by the staff during the reactivity accident that occurred on October 15, 1958. Since 1960, the RB reactor has been modified a few times. Beside the initial natural uranium metal fuel rods, new types of fuel (TVR-S types of Russian origin consisting of 2% enriched uranium metal and 80% enriched UO2 dispersed in aluminum matrix, have been available since 1962 and 1976 respectively. Modifications of the control and safety systems of the reactor were made occasionally. Special reactor cores were designed and constructed using all three types of fuel elements as well as the coupled fast-thermal ones. The Nuclear Safety Committee of the VINĆA Institute, an independent regulatory body, approved for usage all these modifications of the RB reactor on the basis of the Preliminary Safety Analysis Reports, which, beside proposed technical modifications and new regulation rules, included safety analyses of various possible accidents. A special attention was given (and a new safety methodology was proposed to thorough analyses of the design-based accidents related to the coupled fast-thermal cores that included central zones of the reactor filled by the fuel elements without any moderator. In this paper, an overview of some accidents, methodologies and computation tools used for the accident analyses of the RB reactor is given.

  17. Structure of 4-hydrophenylpyruvic acid dioxygenase (HPD) gene and its mutation in tyrosinemic mouse strain III

    Awata, H.; Endo, F.; Matsuda, I. [Kumamoto Univ. Medical School (Japan)] [and others


    4-Hydroxphenylpyruvic acid dioxygenase (HPD) is an important enzyme in tyrosine catabolism in most organisms. The activity of this enzyme is expressed mainly in the liver and is developmentally regulated in mammals. A genetic deficiency of the enzyme in man and mouse leads to hereditary tyrosinemia type 3. Using human HPD cDNA as a probe, a chromosomal gene related to HPD was isolated from human and mouse gene libraries. The human HPD gene is over 30 kilo-bases long and is split into 14 exons. Analysis of the 5{prime} flanking sequence of the gene suggests that expression of the gene is regulated by hepatocyte-specific and liver-enriched transcription factors, as well as by hormones. These features of the 5{prime} flanking region of the gene are similar to those of other genes which are specifically expressed in hepatocytes and which are developmentally regulated. The gene for mouse HPD has a similar structure and we obtained evidence for a nucleotide substitution which generates a termination codon in exon 7 of the HPD gene in III mice. This mutation associates a partial exon skipping and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Thus, mouse strain III can serve as a genetic model for human tyrosinemia type 3. Ongoing studies are expected to elucidate the disease process involved in hereditary tyrosinemia type 1 and to shed light on mechanisms that mediate developmental regulation of HPD gene expression. In addition, mouse strain III together with recently established models for tyrosinemia type 1 will facilitate studies on hereditary tyrosinemias.

  18. 一株产共轭亚油酸瘤胃细菌Streptococcus infantarius RB111的筛选与鉴定%Screening and identification of a Streptococcus infantarius RB111 that produces conjugated linoleic acid

    黄翠丽; 王敏; 成晓杰; 程敏; 仇天雷; 宫春波; 陈强; 高俊莲


    A bacterial strain producing conjugated linoleic acid was isolated from the goat rumen in Erdos, Inner Mongolia, the strain was designated as RB 111 . CLA production by the strain reached 269.2 mg/L,in which the percentage content of cis9, transll-CLA accounted for 52.64% and that of transl0,cis12-CLA accounted for 47.36%. The strain RB111 was identified using its morphological characteristics, fatty acid composition and physiological and biochemical properties, as well as its 16S rRNA gene sequence. The strain RB111 shares 99% sequence identity with the type strain NCDO 599T of Streptococcus infantarius. The result of fatty acid composition analysis revealed that the major fatty acids present in the strain RB111 were C16∶0, C18∶1 w9c and C18∶0, the total account of the three kinds of fatty acids was 60.64%. The morphological characteristics and the results of physiological and biochemical properties of the strain were in well agreement with that of the type strain NCDO 599T of Streptococcus infantarius. On the basis of these data, the strain RB 111 was definited to Streptococcus infantarius.%从内蒙古鄂尔多斯山羊瘤胃中分离筛选到1 株产共轭亚油酸的瘤胃细菌RB111,该菌株的cis9,trans11-CLA和trans10,cis12-CLA总产量为269.2 mg/L,其中cis9,trans11-CLA占52.64%,trans10,cis12-CLA 占47.36%.对菌株RB111 进行了形态学观察、生理生化鉴定、脂肪酸组成分析以及16S rRNA 基因序列分析.16S rRNA 基因序列分析结果表明该菌株与婴儿链球菌(Streptococcus infantarius)的模式菌株NCDO 599 的序列相似性为99%,该菌株的形态特征及生理生化特性与文献报道的Streptococcus infantarius 一致.脂肪酸组成分析结果显示,菌株RB111 的细胞脂肪酸主要成分是C16:0、C18:1 ω9c 和C18:0,3 种脂肪酸占脂肪酸总量的60.64%.综合以上结果,菌株RB111 被鉴定为婴儿链球菌Streptococcus infantarius.

  19. Engaging Students in a Bioinformatics Activity to Introduce Gene Structure and Function

    Barbara J. May


    Full Text Available Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools.  This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools.  Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the putative function of this gene with the use of additional online databases.

  20. Structure, expression pattern and chromosomal localization of the rice Osgrp-2 gene

    LIU; Zongzhi; (刘宗旨); WANG; Jianlong; (王建龙); WANG; Qun; (王群); HUANG; Xun; (黄勋); XU; Weihui; (徐卫辉); ZHU; Lihuang; (朱立煌); HE; Ping; (何平); FANG; Rongxiang; (方荣祥)


    Glycine-rich proteins (GRPs) belong to a kind of important structural proteins of plant cell walls. The expression of GRP genes is regulated spatially and developmentally as well as by various environmental stresses, thus providing a good model for the study of plant gene expression. We obtained the genomic sequence of a new GRP gene (Osgrp-2) from a rice genomic library. The transcription start site of Osgrp-2 was determined by 5'-rapid amplification of cDNA ends (RACE) and a 2.4-kb promoter sequence was thus delimited. The spatial and developmental expression pattern as well as the wound-inducible character of Osgrp-2 in rice plants was analyzed in detail. Furthermore, the gene was mapped onto rice chromosome 10 by analysis of restriction fragment length polymorphism (RFLP).

  1. Reconstruction of Gene Regulatory Networks Based on Two-Stage Bayesian Network Structure Learning Algorithm

    Gui-xia Liu; Wei Feng; Han Wang; Lei Liu; Chun-guang Zhou


    In the post-genomic biology era, the reconstruction of gene regulatory networks from microarray gene expression data is very important to understand the underlying biological system, and it has been a challenging task in bioinformatics. The Bayesian network model has been used in reconstructing the gene regulatory network for its advantages, but how to determine the network structure and parameters is still important to be explored. This paper proposes a two-stage structure learning algorithm which integrates immune evolution algorithm to build a Bayesian network .The new algorithm is evaluated with the use of both simulated and yeast cell cycle data. The experimental results indicate that the proposed algorithm can find many of the known real regulatory relationships from literature and predict the others unknown with high validity and accuracy.

  2. Quorum sensing activity of Serratia fonticola strain RB-25 isolated from an ex-landfill site.

    Ee, Robson; Lim, Yan-Lue; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan


    Quorum sensing is a unique bacterial communication system which permits bacteria to synchronize their behaviour in accordance with the population density. The operation of this communication network involves the use of diffusible autoinducer molecules, termed N-acylhomoserine lactones (AHLs). Serratia spp. are well known for their use of quorum sensing to regulate the expression of various genes. In this study, we aimed to characterized the AHL production of a bacterium designated as strain RB-25 isolated from a former domestic waste landfill site. It was identified as Serratia fonticola using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis and this was confirmed by 16S ribosomal DNA sequencing. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis of S. fonticola strain RB-25 spent culture supernatant indicated the existence of three AHLs namely: N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL) and N-(3-oxohexanoyl) homoserine-lactone (3-oxo-C6 HSL). This is the first report of the production of these AHLs in S. fonticola.

  3. Quorum Sensing Activity of Serratia fonticola Strain RB-25 Isolated from an Ex-landfill Site

    Robson Ee


    Full Text Available Quorum sensing is a unique bacterial communication system which permits bacteria to synchronize their behaviour in accordance with the population density. The operation of this communication network involves the use of diffusible autoinducer molecules, termed N-acylhomoserine lactones (AHLs. Serratia spp. are well known for their use of quorum sensing to regulate the expression of various genes. In this study, we aimed to characterized the AHL production of a bacterium designated as strain RB-25 isolated from a former domestic waste landfill site. It was identified as Serratia fonticola using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF mass spectrometry analysis and this was confirmed by 16S ribosomal DNA sequencing. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis of S. fonticola strain RB-25 spent culture supernatant indicated the existence of three AHLs namely: N-butyryl-L-homoserine lactone (C4-HSL, N-hexanoyl-L-homoserine lactone (C6-HSL and N-(3-oxohexanoyl homoserine-lactone (3-oxo-C6 HSL. This is the first report of the production of these AHLs in S. fonticola.

  4. p38α controls erythroblast enucleation and Rb signaling in stress erythropoiesis

    Simon M Schultze; Andreas Mairhofer; Dan Li; Jin Cen; Hartmut Beug; Erwin F Wagner; Lijian Hui


    Enucleation of erythroblasts during terminal differentiation is unique to mammals.Although erythroid enucleation has been extensively studied,only a few genes,including retinoblastoma protein(Rb),have been identified to regulate nuclear extrusion.It remains largely undefined by which signaling molecules,the extrinsic stimuli,such as erythropoietin(Epo),are transduced to induce enucleation.Here,we show that p38α,a mitogen-activated protein kinase(MAPK),is required for erythroid enucleation.In an ex vivo differentiation system that contains high Epo levels and mimics stress erythropoiesis,p38α is activated during erythroid differentiation.Loss of p38α completely blocks enucleation of primary erythroblasts.Moreover,p38α regulates erythroblast enucleation in a cell-autonomous manner in vivo during fetal and anemic stress erythropoiesis.Markedly,loss of p38α leads to downregulation of p21,and decreased activation of the p21 target Rb,both of which are important regulators of erythroblast enucleation.This study demonstrates that p38α is a key signaling molecule for erythroblast enucleation during stress erythropoiesis.

  5. Frequent disruption of the RB1 pathway in diffuse large B cell lymphoma

    Møller, Michael Boe; Kania, P W; Ino, Y


    downstream of exon 3 generating a novel splice signal. Seven tumours (21%) showed cyclin D3 overexpression, including all three thyroid lymphomas (P = 0.006). Cyclin D3 overexpression and p16INK4A/pRb aberrations were mutually exclusive, supporting an oncogenic role for cyclin D3 in DLCL. p16INK4A...... expression was associated with treatment failure (P = 0.020), and multivariate analysis of overall survival identified both low E2F-1 expression (relative risk = 6.9; P = 0.0037) and p16INK4A inactivation (relative risk = 3.3; P = 0.0247) as independent prognostic markers. These data support a role of E2F-1...... as tumour suppressor gene in lymphoma and strongly suggest that the RB1 and p53 pathways are important in the development of de novo DLCL. Furthermore, low E2F-1 expression and p16INK4A inactivation may serve as prognostic markers for patients with this type of lymphoma....

  6. Fine structure analysis of the WT1 gene in sporadic Wilms tumors

    Varanasi, R.; Bardeesy, N.; Ghahremani, M.; Pelletier, J. [McGill Univ., Montreal (Canada); Petruzzi, M.-J.; Nowak, N.; Shows, T.B. [State Univ. of New York, Buffalo, NY (United States); Adam, M.A. [Merck-Frosst Center for Therapeutic Research, Point Claire-Dorval (Canada); Grundy, P. [Cross Cancer Institute, Edmonton (Canada)


    Molecular genetic studies indicate that the etiology of Wilms tumor (WT) is complex, involving at least three loci. Germ-line mutations in the tumor suppressor gene, WT1, have been documented in children with WTs and urogenital developmental anomalies. Sporadic tumors constitute the majority (>90%) of WT cases and previous molecular analyses of the WT1 gene have focused only on the DNA-binding domain. Using the single-strand conformational polymorphism (SSCP) assay, the authors analyzed the structural integrity of the entire WT1 gene in 98 sporadic WTs. By PCR-SSCP they find that mutations in the WT1 gene are rare, occurring in only six tumors analyzed. In one sample, two independent intragenic mutations inactivated both WT1 alleles, providing a singular example of two different somatic alterations restricted to the WT1 gene. This case is consistent with the existence of only one tumor suppressor gene at 11p13 involved in the pathogenesis of WTs. The data, together with the previously ascertained occurrence of large deletions/insertions in WT1, define the frequency at which the WT1 gene is altered in sporadic tumors. 36 refs., 3 figs.

  7. The mouse Fau gene: genomic structure, chromosomal localization, and characterization of two retropseudogenes.

    Casteels, D; Poirier, C; Guénet, J L; Merregaert, J


    The Fau gene is the cellular homolog of the fox sequence of the Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV). FBR-MuSV acquired the Fau gene by transduction in a transcriptional orientation opposite to that of the genomic Fau gene. The genomic structure of the mouse Fau gene (MMFAU) and its upstream elements have been determined and are similar to those of the human FAU gene. The gene consists of five exons and is located on chromosome 19. The first exon is not translated. The promoter region has no well-defined TATA box but contains the polypyrimidine initiator flanked by regions of high GC content (65%) and shows all of the characteristics of a housekeeping gene. The 5' end of the mRNA transcript was determined by 5' RACE analysis and is located, as expected, in the polypyrimidine initiator site. Furthermore, the sequences of two retropseudogenes (Fau-ps1 and Fau-ps2) are reported. Both pseudogenes are approximately 75% identical to the Fau cDNA, but both are shorter due to a deletion at the 5' end and do not encode a functional protein. Fau-prs is interrupted by an AG-rich region of about 350 bp within the S30 region of the Fau cDNA. Fau-ps1 was localized on chromosome 1 and Fau-ps2 on chromosome 7.

  8. Evidence-based gene models for structural and functional annotations of the oil palm genome.

    Chan, Kuang-Lim; Tatarinova, Tatiana V; Rosli, Rozana; Amiruddin, Nadzirah; Azizi, Norazah; Halim, Mohd Amin Ab; Sanusi, Nik Shazana Nik Mohd; Jayanthi, Nagappan; Ponomarenko, Petr; Triska, Martin; Solovyev, Victor; Firdaus-Raih, Mohd; Sambanthamurthi, Ravigadevi; Murphy, Denis; Low, Eng-Ti Leslie


    Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA

  9. qPCR for Second Year Undergraduates: A Short, Structured Inquiry to Illustrate Differential Gene Expression

    McCauslin, Christine Seitz; Gunn, Kathryn Elaine; Pirone, Dana; Staiger, Jennifer


    We describe a structured inquiry laboratory exercise that examines transcriptional regulation of the "NOS2" gene under conditions that simulate the inflammatory response in macrophages. Using quantitative PCR and the comparative C[subscript T] method, students are able determine whether transcriptional activation of "NOS2"…

  10. Localization to Chromosomes of Structural Genes for the Major Protease Inhibitors of Barley Grains

    Hejgaard, Jørn; Bjørn, S.E.; Nielsen, Gunnar Gissel


    Wheat-barley chromosome addition lines were compared by isoelectric focusing of protein extracts to identify chromosomes carrying loci for the major immunochemically distinct protease inhibitors of barley grains. Structural genes for the following inhibitors were localized: an inhibitor of both...

  11. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)


    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a

  12. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)


    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a distinc

  13. Structure and gene cluster of the o-antigen of Escherichia coli o96.

    Guo, Xi; Senchenkova, Sof'ya N; Shashkov, Alexander S; Perepelov, Andrei V; Liu, Bin; Knirel, Yuriy A


    Mild acid degradation of the lipopolysaccharide of Escherichia coli O96 afforded a mixture of two polysaccharides. The following structure of the pentasaccharide repeating unit of the major polymer was established by sugar analysis, Smith degradation, and (1)H and (13)C NMR spectroscopy: [Formula: see text]. The O-antigen gene