FAK acts as a suppressor of RTK-MAP kinase signalling in Drosophila melanogaster epithelia and human cancer cells

Receptor Tyrosine Kinases (RTKs) and Focal Adhesion Kinase (FAK) regulate multiple signalling pathways, including mitogen-activated protein (MAP) kinase pathway. FAK interacts with several RTKs but little is known about how FAK regulates their downstream signalling. Here we investigated how FAK regulates signalling resulting from the overexpression of the RTKs RET and EGFR. FAK suppressed RTKs signalling in Drosophila melanogaster epithelia by impairing MAPK pathway. This regulation was also observed in MDA-MB-231 human breast cancer cells, suggesting it is a conserved phenomenon in humans. Mechanistically, FAK reduced receptor recycling into the plasma membrane, which resulted in lower MAPK activation. Conversely, increasing the membrane pool of the receptor increased MAPK pathway signalling. FAK is widely considered as a therapeutic target in cancer biology; however, it also has tumour suppressor properties in some contexts. Therefore, the FAK-mediated negative regulation of RTK/MAPK signalling described here may have potential implications in the designing of therapy strategies for RTK-driven tumours

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research

The Fifth Data Release of the Sloan Digital Sky Survey

This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and represents the completion of the SDSS-I project (whose successor, SDSS-II will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 square degrees, and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 square degrees of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS Sixth Data Release (DR6) is now public, available from http://www.sdss.or

A Weakened Transcriptional Enhancer Yields Variegated Gene Expression

Identical genes in the same cellular environment are sometimes expressed differently. In some cases, including the immunoglobulin heavy chain (IgH) locus, this type of differential gene expression has been related to the absence of a transcriptional enhancer. To gain additional information on the role of the IgH enhancer, we examined expression driven by enhancers that were merely weakened, rather than fully deleted, using both mutations and insulators to impair enhancer activity. For this purpose we used a LoxP/Cre system to place a reporter gene at the same genomic site of a stable cell line. Whereas expression of the reporter gene was uniformly high in the presence of the normal, uninsulated enhancer and undetectable in its absence, weakened enhancers yielded variegated expression of the reporter gene; i.e., the average level of expression of the same gene differed in different clones, and expression varied significantly among cells within individual clones. These results indicate that the weakened enhancer allows the reporter gene to exist in at least two states. Subtle aspects of the variegation suggest that the IgH enhancer decreases the average duration (half-life) of the silent state. This analysis has also tested the conventional wisdom that enhancer activity is independent of distance and orientation. Thus, our analysis of mutant (truncated) forms of the IgH enhancer revealed that the 250 bp core enhancer was active in its normal position, ∼1.4 kb 3′ of the promoter, but inactive ∼6 kb 3′, indicating that the activity of the core enhancer was distance-dependent. A longer segment – the core enhancer plus ∼1 kb of 3′ flanking material, including the 3′ matrix attachment region – was active, and the activity of this longer segment was orientation-dependent. Our data suggest that this 3′ flank includes binding sites for at least two activators

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Spin chemistry investigation of peculiarities of photoinduced electron transfer in donor-acceptor linked system

Photoinduced intramolecular electron transfer in linked systems, (R,S)- and (S,S)-naproxen-N-methylpyrrolidine dyads, has been studied by means of spin chemistry methods [magnetic field effect and chemically induced dynamic nuclear polarization (CIDNP)]. The relative yield of the triplet state of the dyads in different magnetic field has been measured, and dependences of the high-field CIDNP of the N-methylpyrrolidine fragment on solvent polarity have been investigated. However, both (S,S)- and (R,S)-enantiomers demonstrate almost identical CIDNP effects for the entire range of polarity. It has been demonstrated that the main peculiarities of photoprocesses in this linked system are connected with the participation of singlet exciplex alongside with photoinduced intramolecular electron transfer in chromophore excited state quenching.This work was supported by the grants 08-03-00372 and 11-03-01104 of the Russian Foundation for Basic Research, and the grant of Priority Programs of the Russian Academy of Sciences, nr. 5.1.5.Magin, I.; Polyakov, N.; Khramtsova, E.; Kruppa, A.; Stepanov, A.; Purtov, P.; Leshina, T.... (2011). Spin chemistry investigation of peculiarities of photoinduced electron transfer in donor-acceptor linked system. Applied Magnetic Resonance. 41(2-4):205-220. https://doi.org/10.1007/s00723-011-0288-3S205220412-4J.S. Park, E. Karnas, K. Ohkubo, P. Chen, K.M. Kadish, S. Fukuzumi, C.W. Bielawski, T.W. Hudnall, V.M. Lynch, J.L. Sessler, Science 329, 1324–1327 (2010)S.Y. Reece, D.G. Nocera, Annu. Rev. Biochem. 78, 673–699 (2009)M.S. Afanasyeva, M.B. Taraban, P.A. Purtov, T.V. Leshina, C.B. Grissom, J. Am. Chem. Soc. 128, 8651–8658 (2006)M.A. Fox, M. Chanon, in Photoinduced Electron Transfer. C: Photoinduced Electron Transfer Reactions: Organic Substrates (Elsevier, New York, 1988), p. 754P.J. Hayball, R.L. Nation, F. Bochner, Chirality 4, 484–487 (1992)N. Suesa, M.F. Fernandez, M. Gutierrez, M.J. Rufat, E. Rotllan, L. Calvo, D. Mauleon, G. Carganico, Chirality 5, 589–595 (1993)A.M. Evans, J. Clin. Pharmacol. 36, 7–15 (1996)Y. Inoue, T. Wada, S. Asaoka, H. Sato, J.-P. Pete, Chem Commun. 4, 251–259 (2000)T. Yorozu, K. Hayashi, M. Irie, J. Am. Chem. Soc. 103, 5480–5548 (1981)N.J. Turro, in Modern Molecular Photochemistry (Benjamin/Cummings, San Francisco, 1978)K.M. Salikhov, Y.N. Molin, R.Z. Sagdeev, A.L. Buchachenko, in Spin Polarization and Magnetic Field Effects in Radical Reactions (Akademiai Kiado, Budapest, 1984), p. 419E.A. Weiss, M.A. Ratner, M.R. Wasielewski, J. Phys. Chem. A 107, 3639–3647 (2003)A.S. Lukas, P.J. Bushard, E.A. Weiss, M.R. Wasielewski, J. Am. Chem. Soc. 125, 3921–3930 (2003)R. Nakagaki, K. Mutai, M. Hiramatsu, H. Tukada, S. Nakakura, Can. J. Chem. 66, 1989–1996 (1988)M.C. Jim′enez, U. Pischel, M.A. Miranda, J. Photochem. Photobiol. C Photochem. Rev. 8, 128–142 (2007)S. Abad, U. Pischel, M.A. Miranda, Photochem. Photobiol. Sci. 4, 69–74 (2005)U. Pischel, S. Abad, L.R. Domingo, F. Bosca, M.A. Miranda, Angew. Chem. Int. Ed. 42, 2531–2534 (2003)G.L. Closs, R.J. Miller, J. Am. Chem. Soc. 101, 1639–1641 (1979)G.L. Closs, R.J. Miller, J. Am. Chem. Soc. 103, 3586–3588 (1981)M. Goez, Chem. Phys. Lett. 188, 451–456 (1992)I.F. Molokov, Y.P. Tsentalovich, A.V. Yurkovskaya, R.Z. Sagdeev, J. Photochem. Photobiol. A 110, 159–165 (1997)U. Pischel, S. Abad, M.A. Miranda, Chem. Commun. 9, 1088–1089 (2003)H. Hayashi, S. Nagakura, Bull. Chem. Soc. Jpn. 57, 322–328 (1984)Y. Sakaguchi, H. Hayashi, S. Nagakura, Bull. Chem. Soc. Jpn. 53, 39–42 (1980)H. Yonemura, H. Nakamura, T. Matsuo, Chem. Phys. Lett. 155, 157–161 (1989)N. Hata, M. Hokawa, Chem. Lett. 10, 507–510 (1981)M. Shiotani, L. Sjoeqvist, A. Lund, S. Lunell, L. Eriksson, M.B. Huang, J. Phys. Chem. 94, 8081–8090 (1990)E. Schaffner, H. Fischer, J. Phys. Chem. 100, 1657–1665 (1996)Y. Mori, Y. Sakaguchi, H. Hayashi, Chem. Phys. Lett. 286, 446–451 (1998)I.M. Magin, A.I. Kruppa, P.A. Purtov, Chem. Phys. 365, 80–84 (2009)K.K. Barnes, Electrochemical Reactions in Nonaqueous Systems (M. Dekker, New York, 1970), p. 560J. Bargon, J. Am. Chem. Soc. 99, 8350–8351 (1977)M. Goez, I. Frisch, J. Phys. Chem. A 106, 8079–8084 (2002)A.K. Chibisov, Russ. Chem. Rev. 50, 615–629 (1981)J. Goodman, K. Peters, J. Am. Chem. Soc. 107, 1441–1442 (1985)H. Cao, Y. Fujiwara, T. Haino, Y. Fukazawa, C.-H. Tung, Y. Tanimoto, Bull. Chem. Soc. Jpn. 69, 2801–2813 (1996)P.A. Purtov, A.B. Doktorov, Chem. Phys. 178, 47–65 (1993)A.I. Kruppa, O.I. Mikhailovskaya, T.V. Leshina, Chem. Phys. Lett. 147, 65–71 (1988)M.E. Michel-Beyerle, R. Haberkorn, W. Bube, E. Steffens, H. Schröder, H.J. Neusser, E.W. Schlag, H. Seidlitz, Chem. Phys. 17, 139–145 (1976)K. Schulten, H. Staerk, A. Weller, H.-J. Werner, B. Nickel, Z. Phys. Chem. 101, 371–390 (1976)K. Gnadig, K.B. Eisenthal, Chem. Phys. Lett. 46, 339–342 (1977)T. Nishimura, N. Nakashima, N. Mataga, Chem. Phys. Lett. 46, 334–338 (1977)M.G. Kuzmin, I.V. Soboleva, E.V. Dolotova, D.N. Dogadkin, High Eng. Chem. 39, 86–96 (2005

Association between promoter -1607 polymorphism of MMP1 and Lumbar Disc Disease in Southern Chinese

<p>Abstract</p> <p>Background</p> <p>Matrix metalloproteinases (MMPs) are involved in the degradation of the extracellular matrix of the intervertebral disc. A SNP for guanine insertion/deletion (G/D), the -1607 promoter polymorphism, of the <it>MMP1 </it>gene was found significantly affecting promoter activity and corresponding transcription level. Hence it is a good candidate for genetic studies in DDD.</p> <p>Methods</p> <p>Southern Chinese volunteers between 18 and 55 years were recruited from the population. DDD in the lumbar spine was defined by MRI using Schneiderman's classification. Genomic DNA was isolated from the leukocytes and genotyping was performed using the Sequenom^®platform. Association and Hardy-Weinberg equilibrium checking were assessed by Chi-square test and Mann-Whitney U test.</p> <p>Results</p> <p>Our results showed substantial evidence of association between -1607 promoter polymorphism of <it>MMP1 </it>and DDD in the Southern Chinese subjects. D allelic was significantly associated with DDD (p value = 0.027, odds ratio = 1.41 with 95% CI = 1.04–1.90) while Genotypic association on the presence of D allele was also significantly associated with DDD (p value = 0.046, odds ratio = 1.50 with 95% CI = 1.01–2.24). Further age stratification showed significant genotypic as well as allelic association in the group of over 40 years (genotypic: p value = 0.035, odds ratio = 1.617 with 95% CI = 1.033–2.529; allelic: p value = 0.033, odds ratio = 1.445 with 95% CI = 1.029–2.029). Disc bulge, annular tears and the Schmorl's nodes were not associated with the D allele.</p> <p>Conclusion</p> <p>We demonstrated that individuals with the presence of D allele for the -1607 promoter polymorphism of <it>MMP1 </it>are about 1.5 times more susceptible to develop DDD when compared with those having G allele only. Further association was identified in individuals over 40 years of age. Disc bulge, annular tear as well as Schmorl's nodes were not associated with this polymorphism.</p

Stat3 and c-Myc Genome-Wide Promoter Occupancy in Embryonic Stem Cells

Embryonic stem (ES) cell pluripotency is regulated in part by transcription factor (TF) pathways that maintain self-renewal and inhibit differentiation. Stat3 and c-Myc TFs are essential for maintaining mouse ES cell self-renewal. c-Myc, together with Oct4, Sox2, and Klf4, is a reprogramming factor. While previous studies have investigated core transcriptional circuitry in ES cells, other TF pathways that promote ES cell pluripotency have yet to be investigated. Therefore, to further understand ES cell transcriptional networks, we used genome-wide chromatin immunoprecipitation and microarray analysis (ChIP-chip) to map Stat3 and c-Myc binding targets in ES cells. Our results show that Stat3 and c-Myc occupy a significant number of genes whose expression is highly enriched in ES cells. By comparing Stat3 and c-Myc target genes with gene expression data from undifferentiated ES cells and embryoid bodies (EBs), we found that Stat3 binds active and inactive genes in ES cells, while c-Myc binds predominantly active genes. Moreover, the transcriptional states of Stat3 and c-Myc targets are correlated with co-occupancy of pluripotency-related TFs, polycomb group proteins, and active and repressive histone modifications. We also provide evidence that Stat3 targets are differentially expressed in ES cells following removal of LIF, where culture of ES cells in the absence of LIF resulted in downregulation of Stat3 target genes enriched in ES cells, and upregulation of lineage specific Stat3 target genes. Altogether, we reveal transcriptional targets of two key pluripotency-related genes in ES cells – Stat3 and c-Myc, thus providing further insight into the ES cell transcriptional network