http://precedings.nature.com/subjects/molecular-cell-biology/ Recently posted documents in Molecular Cell Biology Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3968/version/1 Nine-amino-acid transactivation domain, 9aaTAD, defines a large superfamily of yeast and mammals transcription factors. The transactivation of the 9aaTAD has been addressed to multiple general co-activators TAF9, MED15, CBP and p300. We demonstrate for the 9aaTAD transcription factors Oaf1 and Gal4 functional and physical interaction with E3-Ubiquitin Ligase Rsp5. The Rsp5-associations with RNA polymerase II and TFIID were reported previously. http://precedings.nature.com/documents/3968/version/1 Mon, 16 Nov 2009 23:52:09 UTC Rsp5 promotes Gene Activation mediated by 9aaTAD Transcription Factors Oaf1 and Gal4 hdl:10101/npre.2009.3968.1 2009-11-16 Joachim Lipp Nature Precedings 2009-11-16T23:52:09Z Manuscript Genetics & Genomics Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3954.1 In an era of nutraceuticular research, ‘Noni’ fruit is considered as a panacea because of the profound claim on its medicinal uses in treating many diseases inclusive of infections of microbial origin. Hence, the present study was done to know the antibacterial activity of aqueous extracts from ripe and unripe fruits of ‘Noni’ Morinda citrifolia L on gastroenteritic and pyogenic bacteria. The study was done for eight gastroenteritic bacteria and six pyogenic bacteria. The estimation of antibacterial activity of the ripe fruit & unripe fruit extract were carried out by serial two fold tube dilution techniques. Minimum Bactericidal Concentration of the ripe as well as unripe fruit extracts for the susceptible bacteria were estimated by Recovery plate method. Both the Unripe and ripe fruit extracts exhibited nearly equal and effective activity. As the unripe fruit is devoid of unpleasant odour, the unripe fruit is preferable over the ripe fruit extract http://dx.doi.org/10.1038/npre.2009.3954.1 Mon, 09 Nov 2009 14:38:04 UTC In Vitro Bactericidal Activities of Extracts From Ripe and Unripe Fruit of ‘Noni’ doi:10.1038/npre.2009.3954.1 2009-11-09 Rajarajan Swaminathan Nature Precedings 2009-11-09T14:38:04Z Manuscript Microbiology Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3931/version/1 Synthetic "microDNAs (MIDs)"is a new class of ~ 20-25 nucleotide-long DNAs capable of repressing the activity of the target gene at the level of transcription by mechanisms that have not been clarified yet. However they are designed to target non-coding regions of the cancer causing genes, thus interfering with transcription. The inhibition might be possible through the direct binding of MIDs to cis-regulatory sites and/or to some Transcription Factors (TF) that normally activate transcription. Synthetic MIDs in some ways are similar to the newly discovered microRNAs a mechanism by which cell regulates its genetic activities at post-transcriptional level. Synthetic MIDs can provide a powerful tool to prevent massive production of mRNA by undesired gene activities. Therefore drugs are not required to interact with overwhelming number of mRNA and microRNA copies that may present unwanted side effects. In vitro studies suggest that the inhibition of the target gene starts after the first round of DNA replication, usually 24 hours after treatment depending on cell doubling time. Cell growth suppression maximizes at day 6 or 7 and the inhibition effect is sustained for weeks. We have shown that blocking of both bcl-2 and k-ras transcription by their specific microDNA Inhibitors induced apoptosis in HL60 leukemia cells and B-cell lymphomas. http://precedings.nature.com/documents/3931/version/1 Wed, 04 Nov 2009 10:28:46 UTC MicroDNAs and Transcriptional Regulation hdl:10101/npre.2009.3931.1 2009-11-04 Nature Precedings 2009-11-04T10:28:46Z Manuscript Cancer Genetics & Genomics Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3860.1 Stuart Hameroff has wrongly estimated that a typical brain neuron has 107 tubulin dimers and wrongly attributed this result to Yu and Baas, J. Neurosci. 1994; 14: 2818-2829. In this letter we show that Hameroff’s estimate is based on misunderstanding of the results provided by Yu and Baas, who actually measured the total microtubule length in a single axonal projection with length of 56 μm in a differentiating in vitro stage 3 embryonic hippocampal neuron. In order to visualize how big Hameroff’s error is, we have reconstructed two of the studied by Yu and Baas embryonic hippocampal neurons with Neuromantic v1.6.3 and compared them with previously published reconstructions of adult hippocampal neurons. Correct calculations show that an adult differentiated pyramidal neuron in vivo has approximately 1.3×109 tubulin dimers incorporated in cytoskeletal microtubules. This estimate has profound implications for the Hameroff-Penrose Orch OR model, because it sets limitations on the number of quantum coherent neurons and implies that if 100% of the neuronal microtubules are quantum coherent for 25 ms then Hameroff-Penrose Orch OR conscious events should involve only 15 pyramidal neurons. http://dx.doi.org/10.1038/npre.2009.3860.1 Wed, 14 Oct 2009 09:31:56 UTC Remarks on the number of tubulin dimers per neuron and implications for Hameroff-Penrose Orch OR doi:10.1038/npre.2009.3860.1 2009-10-14 Nature Precedings 2009-10-14T09:31:56Z Manuscript Molecular Cell Biology Neuroscience http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3828/version/1 Limusaurus is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II & III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, & IV in other amniotes. Limusaurus has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, & IV, thus explaining the embryological position of bird wing digits. However, morphology and gene expression of the anterior bird wing digit specifically resemble digit I, not II, of other amniotes. We argue that digit I loss in Limusaurus is derived and thus irrelevant to understanding the development of the bird wing. http://precedings.nature.com/documents/3828/version/1 Tue, 06 Oct 2009 12:15:57 UTC Limusaurus and bird digit identity hdl:10101/npre.2009.3828.1 2009-10-06 Alexander O. Vargas Nature Precedings 2009-10-06T12:15:57Z Manuscript Developmental Biology Genetics & Genomics Molecular Cell Biology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3718/version/1 The discovery of microRNAs (miRNAs) as a new class of regulators of gene expression has triggered an explosion of research, but has left many unanswered questions about how this regulation works and how it is integrated with other regulatory mechanisms. A number of miRNAs have been found to be present in blood plasma and other body fluids of humans and mice in surprisingly high concentrations. This observation was unexpected in two respects: first, the fact that these molecules are present at all outside the cell at significant concentrations; and second, that these molecules appear to be stable outside of the cell. In light of this it has been suggested that the biological function of miRNAs may also extend outside of the cell and mediate cell-cell communication[1-5]. Such a system would be expected to export specific miRNAs from cells in response to specific biological stimuli. We report here that after serum deprivation several human cell lines tested do export a spectrum of miRNAs into the culture medium. The export response is substantial and prompt. The exported miRNAs are found both within and outside of microvesicles and exosomes. We have identified some candidate protein components of this system outside the cell, and found one exported protein that plays a role in protecting miRNA from degradation. Our results point to a hitherto unrecognized and uncharacterized miRNA trafficking system in mammalian cells that may involve cell-cell communication. http://precedings.nature.com/documents/3718/version/1 Fri, 04 Sep 2009 15:26:49 UTC Mammalian cells in culture actively export specific microRNAs hdl:10101/npre.2009.3718.1 2009-09-04 David J. Galas Nature Precedings 2009-09-04T15:26:49Z Manuscript Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3658/version/1 BackgroundOur bones are remodelled repeatedly during life. A new and “healthy” bone tissue replaces the old one. Accordingly, the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its crystallinity?Methodology/Principal FindingsAcid phosphatase is an enzyme largely expressed by the osteoclasts during resorption and therefore used as a marker of the cells activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimitetically prepared noncrystalline calcium phosphate and nanocrystalline bone resembling calcium apatite. The results showed that both biomimetic samples decreased significantly the enzyme activity while synthetic calcium phosphate samples did not. Consistent with our hypothesis the noncrystalline calcium phosphate had the greater inhibition effect.Conclusions/SignificanceThe in vitro data suggests that the bone-resorbing cells activity could be regulated by the degree of crystallinity of the bone mineral. These findings report that changes in the properties of biogenic inorganic materials induce specific interactions with biomolecules which in turn should define the cell behaviour. These results can establish an interesting mechanism of cell regulation if confirmed in vivo. http://precedings.nature.com/documents/3658/version/1 Thu, 20 Aug 2009 18:20:16 UTC Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study hdl:10101/npre.2009.3658.1 2009-08-20 Yassen Pekounov Nature Precedings 2009-08-20T18:20:16Z Manuscript Chemistry Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3549.1 Multivalent ligands of CD22 for active targeting of B cells. Mary O’Reilly, Wei Hsu Chen, Gladys Completo, Ying Zeng, Satoshi Futakawa and Cory Rillahan and James C. Paulson, Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037The siglecs comprise 13 members of the immunoglobulin superfamily that recognize sialic acid containing glycans, and are differentially expressed on leukocytes and glial cells. The natural ligands of siglecs typically occur on the same cell (in cis) and/or on adjacent cells (in trans). Cis ligands mask the binding of multivalent synthetic sialoside ligands and are thought to regulate the activity of siglecs as modulators of cell signaling. However, synthetic ligands of sufficient avidity can compete with cis ligands, demonstrating a dynamic equilibrium of cis and trans ligand probes. We have explored the relationship between valency, affinity and geometry for achieving avidity sufficient to compete with cis ligands of CD22 (Siglec-2) in situ. A notable achievement is a hetero-bifunctional ligand approach to create multivalent ligands using antibodies as a protein scaffold. The ligand is comprised of a CD22 ligand, 9-biphenylcarboxyl-NeuAcα2-6Galβ1-4GlcNAc (BPCNeuAc), coupled to an antigen, 4-hydroxy-3-nitrophenylacetic acid (NP) (BPCNeuAc-NP). The BPCNeuAc-NP ligand is able to efficiently assemble complexes of anti-NP antibodies with CD22 on both asialo- and native B cells. Surprisingly, assembly of the tertiary complex occurs with anti-NP IgM (n=10), IgA (n=4) and IgG (n=2). The results suggest that spacing of ligands using an antibody optimizes the contribution of geometry to achieve high avidity with low valency. Other multivalent configurations also show promise for targeting B cells. In particular, liposomes bearing BPCNeuAc ligands bind avidly to B cells and are endocytosed. Thus, BPCNeuAc-lipososomes may prove effective in delivery of therapeutic agents to B cells (Supported by NIH grants GM60938, AI50143 ). http://dx.doi.org/10.1038/npre.2009.3549.1 Wed, 05 Aug 2009 08:41:59 UTC Multivalent ligands of CD22 for targeting of B cells doi:10.1038/npre.2009.3549.1 2009-08-05 James C. Paulson Nature Precedings 2009-08-05T08:41:59Z Presentation Biotechnology Cancer Chemistry Immunology Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3436/version/1 The interconnection between vision and somatosensation is already well-established and is further supplemented by the evolutionary link between eyes and photoreceptors, and the functional connection between photosensation and thermoreception. However, our analysis hypothesizes a possibility that vision is not just linked to somatosensation, but may not exist without somatosensation. Surprisingly, our photoreceptor itself needs somatosensory proteins for its functioning, and our entire visual pathway depends on somatosensory cues for its functioning. http://precedings.nature.com/documents/3436/version/1 Fri, 17 Jul 2009 14:46:25 UTC Can Vision Exist Without Somatosensation? hdl:10101/npre.2009.3436.1 2009-07-17 Manivannan Muniyandi Nature Precedings 2009-07-17T14:46:25Z Manuscript Molecular Cell Biology Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3419.1 Melanosomes are lysosome-related organelles that produce and transport the pigment melanin within melanocytes. Mutations in proteins required for melanosome transport and formation lead to a range of pigmentation defects, manifested at the cellular level as perinuclear clustering of melanosomes, or reduced sorting of melanosomal cargo such as tyrosinase-related protein 1 (TYRP1). A pilot screen was carried out to investigate whether a combination of cellular imaging and RNA interference could be used to identify new proteins involved in pigmentation pathways. In this study, eleven genes known to play a role in melanosome transport/formation or other pigmentation properties were knocked down in mouse melanocytes with shRNAmir constructs. The investigated genes were TYRP1, pallidin, cappuccino, dysbindin, HPS5, LYST, Myosin Va, melanophilin, RhoA, UBPY and mahogunin. In a blinded confocal imaging experiment, the only reproducible change observed in cells in which these targets were knocked down was a decrease in TYRP1 levels upon transfection with knockdown constructs against TYRP1 itself, or one of three constructs targeting HPS5 (Hermansky-Pudlak Syndrome 5). Upon analysis with high-content imaging software, only the knockdown construct against TYRP1 itself was detected. RT-PCR analysis showed that many of the shRNAmir constructs did not reduce mRNA and proteins levels enough to detect effects on melanosome properties. This was further examined for melanophilin, a protein necessary for melanosome transport. Altogether, the data show that this system is currently not sensitive enough for use in a screen for unknown regulators of melanosome transport and formation. The main obstacle appears to be incomplete reduction of target protein levels. Our observation that a ~50% reduction in mRNA level is not sufficient to elicit an effect is supported by the fact that heterozygous carriers of melanosomal transport disorders (Griscelli Syndrome, Hermansky-Pudlak Syndrome) do not display diseases phenotypes. A further reduction in protein levels, for example by viral infection of shRNA, may be required. http://dx.doi.org/10.1038/npre.2009.3419.1 Tue, 14 Jul 2009 10:19:29 UTC Technical Note: The Use of RNA-interference as a Tool to Find Proteins Involved in Melanosome Formation or Transport doi:10.1038/npre.2009.3419.1 2009-07-14 Eva M. Amsen Nature Precedings 2009-07-14T10:19:29Z Manuscript Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/