Alterations in the cell cycle of Drosophila imaginal disc cells precede metamorphosis

Flow cytometric analyses of imaginal disc and brain nuclei of Drosophila melanogaster have been made throughout the third larval instar. In wing, haltere, and leg discs the proportion of cells in the G₂M phase of the cell cycle (tetraploid cells) increases with larval age. In contrast, in the eye disc and in brain the proportion of tetraploid cells, already low at the outset of the instar, declines further. Measurement of growth rates for disc and brain tissue during the same developmental period was carried out by the cell counting procedure of Martin (1982). Our results are consistent with the conclusion that imaginal discs grow exponentially with an apparent doubling time of 5–10 hr from the resumption of cell division (in the first or second larval instar) until about 95 hr, when the apparent doubling time increases. Cell numbers increase until at least 5 hr after formation of white prepupae (122 hr), but during the preceding 10 hr the rate of increase is low. Thus, for wing and leg discs, but not for the eye disc and brain, the declining growth rate is associated with an increase in the proportions of tetraploid cells. In conjunction with cell counts and flow cytometry, fluorometric determination of disc DNA content at 112 hr indicated that the diploid DNA content of imaginal disc nuclei is 0.45 pg.     

Exploring the Role of Integral Membrane Proteins in ATP-Binding Cassette Transporters: Analysis of a Collection of MalG Insertion Mutants

The maltose transport complex of Escherichia coli is a well-studied example of an ATP-binding cassette transporter. The complex, containing one copy each of the integral membrane proteins MalG and MalF and two copies of the peripheral cytoplasmic membrane protein MalK, interacts with the periplasmic maltose-binding protein to efficiently translocate maltose and maltodextrins across the bacterial cytoplasmic membrane. To investigate the role of MalG both in MalFGK₂ assembly interactions and in subsequent transport interactions, we isolated and characterized 18 different MalG mutants, each containing a 31-residue insertion in the protein. Eight insertions mapping to distinct hydrophilic regions of MalG permitted either assembly or both assembly and transport interactions to occur. In particular, we isolated two insertions mapping to extracytoplasmic (periplasmic) regions of MalG which preserved both assembly and transport abilities, suggesting that these are permissive sites in the protein. Another periplasmic insertion seems to affect only transport-specific interactions between MalG and maltose-binding protein, defining a novel class of MalG mutants. Finally, four MalG mutant proteins, although stably expressed, are unable to assemble into the MalFGK₂ complex. These mutants contain insertions in only two different hydrophilic regions of MalG, consistent with the notion that a restricted number of domains in this protein are critical complex assembly determinants. These MalG mutants will allow us to further explore the intermolecular interactions of this model transporter.Integral membrane proteins play a central role in the ATP-binding cassette (ABC) transporter superfamily, whose prokaryotic and eukaryotic members traffic a variety of substrates such as ions, sugars, amino acids, peptides, and proteins (15). This large family of transporters is defined by a conserved cytoplasmic ATPase component and integral membrane domains which interact to carry out the specific transport process (4, 15). Among the eukaryotic members are such medically relevant proteins as the P-glycoprotein implicated in multidrug-resistant cancer cells, the cystic fibrosis transmembrane regulator protein, and the human peroxisomal adrenoleukodystrophy protein (2, 34, 35). Among the prokaryotic members of the ABC superfamily are the periplasmic binding protein-dependent transporters. These family members are characterized by a conserved region of the integral membrane component(s) in addition to the conserved cytoplasmic ATPase (4). One member of this prokaryotic subgroup, the maltose transport complex of Escherichia coli, presents a useful model for the integral membrane folding and assembly interactions required for ABC transporters. The maltose transport complex consists of the integral membrane proteins MalF and MalG and a peripheral cytoplasmic membrane ATPase, MalK (reviewed in reference 24). These three proteins copurify (11), forming a MalFGK₂ tetrameric complex which acts in concert with the periplasmic maltose-binding protein (MBP), the product of malE, to efficiently translocate maltose and maltodextrins across the bacterial cytoplasmic membrane.MalF has been shown to have eight transmembrane (TM) domains (5), whereas MalG possesses six TM domains (6, 10). Following independent insertion of these proteins into the membrane (22a, 31), assembly of the MalFGK₂ complex is likely mediated by interactions among discrete domains of MalF, MalG, and MalK, resulting in tetramerization (20, 26).Although the specifics of these interactions are unknown, a combination of biochemistry and genetics has allowed for a partial characterization of the complex. Shuman and colleagues isolated and characterized MalF and MalG mutants which enable the MalFGK₂ complex to transport maltose in the absence of MBP (7, 32). These analyses have pointed toward a direct interaction between MBP and periplasmic portions of MalG and MalF (16), between MalG and MalF themselves (7), and between MalK and both MalF and MalG (12). Davidson and Nikaido purified the MalFGK₂ complex and demonstrated extensive chemical cross-linking between MalG and MalF and among MalG, MalF, and MalK (11). Traxler and Beckwith observed that periplasmic loops of MalF become protease resistant only in the presence of MalG and MalK, also suggesting that specific interactions occur among the proteins in the context of an assembled complex (31). Finally, a potentially important MalG-MalK protein interaction signal has been identified in the hydrophilic cytoplasmic loop between the fourth and fifth TM domains of MalG (reference 9; Fig. ​Fig.1).1). This motif is conserved in MalF and in other binding protein-dependent transporters of the ABC superfamily (9, 28) and has been hypothesized to mediate interactions with the conserved ATPase subunit of the complex (17, 22). Open in a separate windowFIG. 1Topology model of MalG. Hydropathy plots and fusion protein analyses (6, 10) suggest that the N and C termini of the 296-residue protein are cytoplasmically localized. The shaded boxes represent putative TM domains, and the shaded amino acids are conserved in integral membrane proteins of periplasmic binding protein-dependent ABC transporters (9, 28). The location of each 31-residue insertion is shown by an arrowhead. The black arrowhead represents an insertion which did not significantly affect MalG transport function, the gray arrowhead depicts partial transport function, and the white arrowheads represent loss of transport ability for the corresponding insertion mutants. Each numbered disc shows the mutant classification of the adjacent insertion mutant (see Discussion for details).Recently, a transposon-mediated insertion mutagenesis technique was developed and used to characterize both permissive and nonpermissive regions of the integral membrane protein LacY (19), as well as the cytoplasmic MalK and LacI proteins (18, 23). These analyses not only identified tolerant hydrophilic regions of each protein but also defined several distinct mutant classes (18, 19, 23). In particular, the phenotypes attributable to the lacI insertion mutations that we isolated were strikingly similar to those of previously characterized amino acid substitutions mapping to the same sites in lacI. Here, we describe the results of this insertion mutagenesis on the MalG protein. This analysis provides a unique in vivo view of the requirements for proper MalG protein folding and of the interactions necessary for MalFGK₂ assembly and maltose transport.     

Error-prone repair and translesion synthesis III: the activation of UmuD (or less is more)

Following DNA damage to Escherichia coli bacteria, RecA protein is activated by binding to single stranded DNA and cleaves its own gene repressor (LexA protein). Two papers from Graham Walker's laboratory showed that several bacterial genes in addition to RecA are repressed by the LexA repressor and are inducible following DNA damage [C.J. Keyon, G.C. Walker, DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli, in: Proceedings of the National Academy of Sciences of the United States of America 77, 1980, pp. 2819--2823] and predicted that one of them (UmuD) might itself be subject to activation by a further cleavage reaction involving activated RecA protein [K.L. Perry, S.J. Elledge, B.B. Mitchell, L. Marsh, G.C. Walker, umuD,C and mucA,B operans whose products are required for UV light- and chemical-induced mutagenesis: UmuD, MucA, and LexA proteins share homology, in: Proceedings of the National Academy of Sciences of the United States of America 82, 1985, pp. 4331--4335]. The processed form of UmuD, termed UmuD', later proved to be a subunit of DNA polymerase V, a key enzyme involved in translesion synthesis.     

Chemical composition of a lipopolysaccharide from Legionella pneumophila

Lipopolysaccharide isolated from Legionella pneumophila (Phil. 1) was examined for chemical composition. The polysaccharide split off by mild acid hydrolysis contained rhamnose, mannose, glucose, quinovosamine, glucosamine and 2-keto-3-deoxyoctonate, in molar proportions 1.6:1.8:1.0:1.5:4.1:2.7. Heptoses were absent and glucose was probably mainly phosphorylated. The carbohydrate backbone of the lipid A part consisted of glucosamine, quinovosamine and glycerol, in the molar ratios 3.9:1.0:3.4, with glycerol as a phosphorylated moiety. A complex fatty acid substitution pattern comprising eight O-ester-linked, exclusively nonhydroxylated acids, and nineteen amide-linked, exclusively 3-hydroxylated acids was revealed. Both straight- and branched (iso and anteiso) carbon chains occurred. The major hydroxy fatty acid was 3-hydroxy-12-methyltridecanoic acid and six others were of a chain-length above 20 carbon atoms, with 3-hydroxy-20-methyldocosanoic acid as the longest. Two dihydroxy fatty acids, 2,3-dihydroxy-12-methyltridecanoic and 2,3-dihydroxytetradecanoic acids, were also detected. These results suggest that L. pneumophila contains a rather complex and unusual lipopolysaccharide structure of considerable biological and chemotaxonomic interest.Abbreviations LPS lipopolysaccharide - PS polysaccharide - KDO 2-keto-3-deoxy-octonate - GC gas chromatography - GC-MS gas chromatograph-mass spectrometer combined instrument - CI chemical ionization - EI electron impact - HF hydrofluoric acid - TFA trifluoroacetyl - TMS trimethylsilyl     

Assessing the magnitude of intra- and interspecific competition in two coral reef fishes

Spatial associations of seven herbivore species in the Kruger National Park, South Africa, are analyzed using a new technique, Correlative Coherence Analysis (CoCA). CoCA is a generalization of the concept of correlation to more than two sequences of numbers. Prior information on the feeding ecology and metabolic requirements of these species is used to contrast spatial scales at which hypothesized guild aggregation or competition occurs. These hypotheses are tested using 13 years of aerial census data collected during the dry season. Our results are consistent with the hypothesis that distributions of large and small species of the same feeding type (i.e., grazers and browsers) overlap in potentially resource-rich areas, but have lower similarity values across all areas because the higher tolerance of large species for low quality foods results in a more even spatial distribution of large species compared to small species.     

Metal complexes of new scorpionate ligands: 2,2′-Bis(pyrazolyl)ethylamine and its derivatives

The new bis(pyrazolyl)amine ligand NH₂CH₂CH(pz)₂ (1) was prepared from the reaction of N-[2,2-bis(pyrazolyl)ethyl]-1,8-naphthalimide with hydrazine monohydrate. A substituted derivative, C₆H₅CH₂NHCH₂CH(pz)₂ (2), was prepared by the reaction of 1 with benzaldehyde followed by reduction with NaBH₄. Ligand 1 was also converted by two methods to the new bitopic, para-linked bis(pyrazolyl)amine ligand p-C₆H₄(CH₂NHCH₂CH(pz)₂)₂, (3). The reactions of the ligands 1-3 with [Cu(PPh₃)₂]NO₃ yields {(PPh₃)Cu[(pz)₂CHCH₂NH₂]}NO₃, {(PPh₃)Cu[(pz)₂CHCH₂NHCH₂C₆H₅]}NO₃ and {[(PPh₃)Cu]₂[p-((pz)₂CHCH₂NHCH₂)₂C₆H₄]}(NO₃)₂·solvate, respectively. Complex {(N₃)₂Cu[(pz)₂CHCH₂NHCH₂C₆H₅]} was obtained from a methanol solution of 2, copper(II) acetate monohydrate and sodium azide. The complex {Cd[(pz)₂CHCH₂NHCH₂C₆H₅]₂}(PF₆)₂·3C₃H₆O was synthesized by reaction of the protonated form of ligand 2, [(pz)₂CHCH₂NH₂CH₂C₆H₅]PF₆, with Cd(acac)₂. In all of the structures the ligands are tridentate, bonding to the metal through the lone pair on the amine group as well as through the pyrazolyl rings - they act as true scorpionates. The solid state structures all have extensive non-covalent interactions, with the N-H functional groups of the amines participating in both N-H?π and N-H?O or N-H?N hydrogen bonding interactions.     

Rapid and reliable high-throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms

We present two methods for DNA extraction from fresh and dried mushrooms that are adaptable to high-throughput sequencing initiatives, such as DNA barcoding. Our results show that these protocols yield ∼85% sequencing success from recently collected materials. Tests with both recent (<2 year) and older (>100 years) specimens reveal that older collections have low success rates and may be an inefficient resource for populating a barcode database. However, our method of extracting DNA from herbarium samples using small amount of tissue is reliable and could be used for important historical specimens. The application of these protocols greatly reduces time, and therefore cost, of generating DNA sequences from mushrooms and other fungi vs. traditional extraction methods. The efficiency of these methods illustrates that standardization and streamlining of sample processing should be shifted from the laboratory to the field.     

Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion

NMR relaxation dispersion measurements report on conformational changes occurring on the μs-ms timescale. Chemical shift information derived from relaxation dispersion can be used to generate structural models of weakly populated alternative conformational states. Current methods to obtain such models rely on determining the signs of chemical shift changes between the conformational states, which are difficult to obtain in many situations. Here, we use a “sample and select” method to generate relevant structural models of alternative conformations of the C-terminal-associated region of Escherichia coli dihydrofolate reductase (DHFR), using only unsigned chemical shift changes for backbone amides and carbonyls (¹H, ¹⁵N, and ¹³C′). We find that CS-Rosetta sampling with unsigned chemical shift changes generates a diversity of structures that are sufficient to characterize a minor conformational state of the C-terminal region of DHFR. The excited state differs from the ground state by a change in secondary structure, consistent with previous predictions from chemical shift hypersurfaces and validated by the x-ray structure of a partially humanized mutant of E. coli DHFR (N23PP/G51PEKN). The results demonstrate that the combination of fragment modeling with sparse chemical shift data can determine the structure of an alternative conformation of DHFR sampled on the μs-ms timescale. Such methods will be useful for characterizing alternative states, which can potentially be used for in silico drug screening, as well as contributing to understanding the role of minor states in biology and molecular evolution.