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Vector And Parameters For Targeted Transgenic Rna Interference In Drosophila Melanogaster, Jian Quan Ni, Michele Markstein, Richard Binari, Barret Pfeiffer, Lu Ping Liu, Christians Villalta, Matthew Booker, Lizabeth Perkins, Norbert Perrimon

Michele Markstein

The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site–driven RNA interference constructs have been inserted into the genome randomly using P-element–mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a transgenic RNA interference vector based on the phiC31 site-specific integration method.

Polybrominated Diphenyl Ethers And Organochlorine Pesticides In Human Milk From Massachusetts, Usa, Kathleen Arcaro, B. Johnson-Restrepo, R. Addink, C. Wong, K. Kannan

Kathleen Arcaro

Concentrations of polybrominated diphenyl ethers (PBDEs), and organochlorine pesticides (OCPs; DDTs, HCHs, CHLs, and HCB) were measured in human breast milk samples collected across Massachusetts, USA, in 2004. Seventeen PBDE congeners were found in the samples, ranging in concentration from 0.06 to 1910 ng g(-1) lipid wt. BDE-47 (2,2',4,4'-tetraBDE), BDE-99 (2,2',4,4',5-pentaBDE), and BDE-100 (2,2',4,4',6-pentaBDE) were the major congeners detected in breast milk samples. Overall mean (+/-SD) concentrations of DDTs, HCHs, CHLs, and HCB were 64.5 +/- 75, 18.9 +/- 19, 32.4 +/- 36, and 2.3 +/- 2.2 ng g(-1) lipid wt, respectively. Concentrations of PBDEs were strongly correlated with concentrations …

Growth Of Thermophilic And Hyperthermophilic Fe(Iii)-Reducing Microorganisms On A Ferruginous Smectite As The Sole Electron Acceptor, Derek Lovley, Kazem Kashefi, Evgenya S. Shelobolina, W. Crawford Elliott

Derek Lovley

Recent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilic Archaea and Bacteria from marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested, Geoglobus ahangari and Geothermobacterium ferrireducens, were not able …

A Rhizosphere Fungus Enhances Arabidopsis Thermotolerance Through Production Of An Hsp90 Inhibitor, Catherine A. Mclellan, Thomas J. Turbyville, E. M. Kithsiri Wijeratne, Arthur Kerschen, Elizabeth Vierling, Christine Queitsch, Luke Whitesell, A. A. Leslie Gunatilaka

Elizabeth Vierling

The molecular chaperone HEAT SHOCK PROTEIN90 (HSP90) is essential for the maturation of key regulatory proteins in eukaryotes and for the response to temperature stress. Earlier, we have reported that fungi living in association with plants of the Sonoran desert produce small molecule inhibitors of mammalian HSP90. Here, we address whether elaboration of the HSP90 inhibitor monocillin I (MON) by the rhizosphere fungus Paraphaeosphaeria quadriseptata affects plant HSP90 and plant environmental responsiveness. We demonstrate that MON binds Arabidopsis (Arabidopsis thaliana) HSP90 and can inhibit the function of HSP90 in lysates of wheat (Triticum aestivum) germ. MON treatment of Arabidopsis seedlings …

Pld1 Is Overexpressed In An Er-Negative Mcf-7 Cell Line Variant And A Subset Of Phospho-Akt-Negative Breast Carcinomas, Kathleen Arcaro, J.M. Gozgit, B.T. Pentecost, S.A. Marconi, C.N. Otis

Kathleen Arcaro

We have used a novel variant of the human oestrogen receptor (ER)-positive MCF-7 cell line, TMX2-28, as a model to study breast cancer. TMX2-28 cells show no detectable levels of mRNA or protein expression for the ER and express basal cytokeratins (CKs) 5, 14, and 17. cDNA microarray comparison between TMX2-28 and its parent cell line, MCF-7, identified 1402 differentially expressed transcripts, one of which was, phospholipase D1 (PLD1). Using real-time RT-PCR, we confirmed that PLD1 mRNA levels are 10-fold higher in TMX2-28 cells than in MCF-7 cells. We next examined PLD1 expression in human breast carcinomas. Phospholipase D1 mRNA …

A Conserved Role For Kinesin-5 In Plant Mitosis, Alex Bannigan, Wolf-Rüdiger Scheible, Wolfgang Lukowitz, Carey Fagerstrom, Patricia Wadsworth, Chris Somerville, Tobias Baskin

Tobias Baskin

The mitotic spindle of vascular plants is assembled and maintained by processes that remain poorly explored at a molecular level. Here, we report that AtKRP125c, one of four kinesin-5 motor proteins in arabidopsis, decorates microtubules throughout the cell cycle and appears to function in both interphase and mitosis. In a temperature-sensitive mutant, interphase cortical microtubules are disorganized at the restrictive temperature and mitotic spindles are massively disrupted, consistent with a defect in the stabilization of anti-parallel microtubules in the spindle midzone, as previously described in kinesin-5 mutants from animals and yeast. AtKRP125c introduced into mammalian epithelial cells by transfection decorates …

Salinity Constraints On Subsurface Archaeal Diversity And Methanogenesis In Sedimentary Rock Rich In Organic Matter, Klaus R. Nusslein, P, J. Waldron, S. T. Petsch, A. M. Martini

Klaus R. Nusslein

The diversity of microorganisms active within sedimentary rocks provides important controls on the geochemistry of many subsurface environments. In particular, biodegradation of organic matter in sedimentary rocks contributes to the biogeochemical cycling of carbon and other elements and strongly impacts the recovery and quality of fossil fuel resources. In this study, archaeal diversity was investigated along a salinity gradient spanning 8 to 3,490 mM Cl− in a subsurface shale rich in CH4 derived from biodegradation of sedimentary hydrocarbons. Shale pore waters collected from wells in the main CH4-producing zone lacked electron acceptors such as O2, NO3−, Fe3+, or SO42−. Acetate …

Genomics And Microarray Analysis Of Aromatics Degradation In Geobacter Metallireducens And Compan To A Geobacter Isolate From A Contaminated Fieldriso Site, Derek Lovley, Jessica E. Butler, Qiang He, Kelly P. Nevin, Zhili He, Jizhong Zhou

Derek Lovley

Background: Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.

Results: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the …

Lack Of Electricity Production By Pelobacter Carbinolicus Indicates That The Capacity For Fe(Iii) Oxide Reduction Does Not Necessarily Confer Electron Transfer Ability To Fuel Cell Anodes, Hanno Richter, Martin Lanthier, Kelly P. Nevin, Derek Lovley

Derek Lovley

The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize …

Lack Of Electricity Production By Pelobacter Carbinolicus Indicates That The Capacity For Fe(Iii) Oxide Reduction Does Not Necessarily Confer Electron Transfer Ability To Fuel Cell Anodes, Hanno Richter, Martin Lanthier, Kelly P. Nevin, Derek Lovley

Kelly Nevin

The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize …

Athol Slaughterhouse Rises From The Ashes, Madeleine K. Charney

Madeleine K. Charney

Plans for rebuilding the Athol slaughterhouse destroyed by fire in 2006.

Roles For Estrogen And Progesterone In Breast Cancer Prevention, D. Joseph Jerry

D. Joseph Jerry

Prevention has long been the holy grail of breast cancer research. The significant reduction in breast cancer risk afforded by a full-term pregnancy early in life suggests the great potential of preventive strategies. In contrast to the risks associated with prolonged exposures, exogenous estrogen and progesterone for short durations can mimic the protective effects of pregnancy in carcinogen-induced mammary tumor models. Rajkumar and coworkers have now demonstrated that these hormones protect mice from mammary tumors initiated by a spectrum of oncogenic alterations that are common in breast cancers. Although differences between rodent models and humans remain, the results reveal that …

Importance Of C-Type Cytochromes For U(Vi) Reduction By Geobacter Sulfurreducens, Evgenya S. Shelobolina, Maddalena V. Coppi, Anton A. Korenevsky, Laurie N. Didonato, Sara A. Sullivan, Hiromi Konishi, Huifang Xu, Ching Leang, Jessica E. Butler, Byoung-Chan Kim, Derek Lovley

Derek Lovley

Background In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated. Results The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50–60%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of …

A High-Performance, Small-Scale Microarray For Expression Profiling Of Many Samples In Arabidopsis-Pathogen Studies, Masano Sato, Raka M. Mitra, John Coller, Dong Wang, Natalie W. Spivey, Julia Dewdney, Carine Denoux, Jane Glazebrook, Fumiaki Katagiri

Dong Wang

Studies of the behavior of biological systems often require monitoring of the expression of many genes in a large number of samples. While whole-genome arrays provide high-quality gene-expression profiles, their high cost generally limits the number of samples that can be studied. Although inexpensive small-scale arrays representing genes of interest could be used for many applications, it is challenging to obtain accurate measurements with conventional small-scale microarrays. We have developed a small-scale microarray system that yields highly accurate and reproducible expression measurements. This was achieved by implementing a stable gene-based quantile normalization method for array-to-array normalization, and a probe-printing design …

Xenopus Tropicalis Egg Extracts Provide Insight Into Scaling Of The Mitotic Spindle, Thomas J. Maresca, M. D. Blower, K. S. Brown, T. C. Grammer, R. M. Harland, R. Heald

Thomas J. Maresca

The African clawed frog Xenopus laevis has been instrumental to investigations of both development and cell biology, but the utility of this model organism for genetic and proteomic studies is limited by its long generation time and unsequenced pseudotetraploid genome. Xenopus tropicalis, which is a small, faster-breeding relative of X. laevis, has recently been adopted for research in developmental genetics and functional genomics, and has been chosen for genome sequencing. We show that X. tropicalis egg extracts reconstitute the fundamental cell cycle events of nuclear formation and bipolar spindle assembly around exogenously added sperm nuclei. Interestingly, X. tropicalis spindles were …

Can You Reduce Tree Height Of Super Spindle Apple Trees With Pruning? Naphthalene Acetic Acid May Help, Wesley Autio, Winfred Cowgill Jr., Jon Clements, James Krupa, Martha Maletta, Rebecca Magron

Wesley Autio

No abstract provided.

An Annual Fire Blight Management Program For Apples, Daniel Cooley, Wesley Autio, Jon Clements

Wesley Autio

No abstract provided.

Final Report From The 2002 Nc-140 Peach Rootstock Trial, Wesley Autio, James Krupa

Wesley Autio

No abstract provided.

Performance Of Mcintosh Apple Trees On Several Geneva And Pillnitz Dwarfing Rootstocks: Nine-Year Summary Of The Massachusetts Planting Of The 1999 Nc-140 Dwarf Apple Rootstock Trial, Wesley Autio, James Krupa, Jon Clements

Wesley Autio

No abstract provided.

Evaluation Of Neo-Tec® For Controlling Nematodes In Golf Greens 2006, Robert L. Wick, L. Stone

Robert L. Wick

No abstract provided.

Analysis Of Est Sequences Suggests Recent Origin Of Allotetraploid Colonial And Creeping Bentgrasses, David Rotter, Arvind K. Bharti, Huaijun Michael Li, Chongyuan Luo, Stacy A. Bonos, Suleiman Bughrara, Geunhwa Jung, Joachim Messing, William A. Meyer, Stephen Rudd, Scott E. Warnke, Faith C. Belanger

Geunhwa Jung

Advances in plant genomics have permitted the analysis of several members of the grass family, including the major domesticated species, and provided new insights into the evolution of the major crops on earth. Two members, colonial bentgrass (Agrostis capillaris L.) and creeping bentgrass (A. stolonifera L.) have only recently been domesticated and provide an interesting case of polyploidy and comparison to crops that have undergone human selection for thousands of years. As an initial step of characterizing these genomes, we have sampled roughly 10% of their gene content, thereby also serving as a starting point for the construction of their …

Mutant Α-Galactosidase A Enzymes Identified In Fabry Disease Patients With Residual Enzyme Activity: Biochemical Characterization And Restoration Of Normal Intracellular Processing By 1-Deoxygalactonojirimycin, Satoshi Ishii, Hui-Hwa Chang, Kunito Kawasaki, Kayo Yasuda, Hui-Li Wu, Scott Garman, Jian-Qiang Fan

Scott Garman

Fabry disease is a lysosomal storage disorder caused by the deficiency of alpha-Gal A (alpha-galactosidase A) activity. In order to understand the molecular mechanism underlying alpha-Gal A deficiency in Fabry disease patients with residual enzyme activity, enzymes with different missense mutations were purified from transfected COS-7 cells and the biochemical properties were characterized. The mutant enzymes detected in variant patients (A20P, E66Q, M72V, I91T, R112H, F113L, N215S, Q279E, M296I, M296V and R301Q), and those found mostly in mild classic patients (A97V, A156V, L166V and R356W) appeared to have normal K(m) and V(max) values. The degradation of all mutants (except E59K) …

Responses Of Rhizobia To Desiccation In Relation To Osmotic Stress, Oxygen, And Temperature, Klaus R. Nusslein, J. A. C Vriezen, F. J. De Bruijn

Klaus R. Nusslein

No abstract provided.

Geonomic And Microarray Analysis Of Aromatics Degradation In Geobacter Metallireducens And Compan To A Geobacter Isolate From A Contaminated Fieldriso Site, Derek Lovley, Jessica E. Butler, Qiang He, Kelly P. Nevin, Zhili He, Jizhong Zhou

Kelly Nevin

Background: Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. Results: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the …

Micromanipulation Studies Of Chromatin Fibers In Xenopus Egg Extracts Reveal Atp-Dependent Nucleosome Assembly Dynamics, Thomas J. Maresca, J. Yan, D. Skoko, R. Heald, J. F. Marko

Thomas J. Maresca

We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening–closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy …

Genetic Mapping In Mice Identifies Dmbt1 As A Candidate Modifier Of Breast Cancer Risk, A. C. Blackburn, L. Z. Hills, A. L. Roberts, J. Wang, D. Aud, J Jung, T. Nikolcheva, J. Allard, G. Peltz, C. N. Otis, Q. J. Cao, R. Ricketts, S.P. Mollenhauer, S. P. Naber, D. Malamud, A. Poustka, D. Joseph Jerry

D. Joseph Jerry

Low-penetrance breast cancer susceptibility alleles seem to play a significant role in breast cancer risk but are difficult to identify in human cohorts. A genetic screen of 176 N2 backcross progeny of two Trp53+/− strains, BALB/c and C57BL/6, which differ in their susceptibility to mammary tumors, identified a modifier of mammary tumor susceptibility in an ∼25-Mb interval on mouse chromosome 7 (designated SuprMam1). Relative to heterozygotes, homozygosity for BALB/c alleles of SuprMam1 significantly decreased mammary tumor latency from 70.7 to 61.1 weeks and increased risk twofold (P = 0.002). Dmbt1 (deleted in malignant brain tumors 1) was identified as a …

A Specific Subset Of Transient Receptor Potential Vanilloid-Type Channel Subunits In Caenorhabditis Elegans Endocrine Cells Function As Mixed Heteromers To Promote Neurotransmitter Release, Antony M. Jose, Amy Bany, Daniel Chase, Michael R. Koelle

Daniel Chase

Transient receptor potential (TRP) channel subunits form homotetramers that function in sensory transduction. Heteromeric channels also form, but their physiological subunit compositions and functions are largely unknown. We found a dominant-negative mutant of the C. elegans TRPV (vanilloid-type) subunit OCR-2 that apparently incorporates into and inactivates OCR-2 homomers as well as heteromers with the TRPV subunits OCR-1 and -4, resulting in a premature egg-laying defect. This defect is reproduced by knocking out all three OCR genes, but not by any single knockout. Thus a mixture of redundant heteromeric channels prevents premature egg laying. These channels, as well as the G-protein …

Ethephon As A Chemical Thinner Of Mcintosh And Macoun Apples In 2007, Wesley Autio, James Krupa

Wesley Autio

No abstract provided.

Linkage Mechanics And Power Amplification Of The Mantis Shrimp's Strike, Sheila Patek, B. N. Nowroozi, J. E. Baio, R. L. Caldwell, A. P. Summers

Sheila Patek

Mantis shrimp (Stomatopoda) generate extremely rapid and forceful predatory strikes through a suite of structural modifications of their raptorial appendages. Here we examine the key morphological and kinematic components of the raptorial strike that amplify the power output of the underlying muscle contractions. Morphological analyses of joint mechanics are integrated with CT scans of mineralization patterns and kinematic analyses toward the goal of understanding the mechanical basis of linkage dynamics and strike performance. We test whether a four-bar linkage mechanism amplifies rotation in this system and find that the rotational amplification is approximately two times the input rotation, thereby amplifying …

The Acoustic Mechanics Of Stick–Slip Friction In The California Spiny Lobster (Panulirus Interruptus), Sheila Patek, J. E. Baio

Sheila Patek

The dynamic interplay between static and sliding friction is fundamental to many animal movements. One interesting example of stick–slip friction is found in the sound-producing apparatus of many spiny lobster species (Palinuridae). The acoustic movements of the spiny lobster's plectrum over the file are generated by stick–slip friction between the two surfaces. We examined the microscopic anatomy, kinematics, acoustics and frictional properties of the California spiny lobster (Panulirus interruptus) toward the goal of quantitatively characterizing the frictional and acoustic mechanics of this system. Using synchronous high-speed video and sound recordings, we tested whether plectrum kinematics are correlated with acoustic signal …