NMR structure shows that the SARS-unique domain contains a macrodomain fold

The NMR structure of a central segment of the previously annotated "SARS-unique domain" (SUD-M; "middle of the SARS-unique domain") in the SARS coronavirus (SARS-CoV) non-structural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3-residues 528-648, and there is a flexibly extended N-terminal tail with the residues 513-527 and a C-terminal flexible tail of residues 649-651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527-651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly-A and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows 3D structure homology with several helicases and NTP-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Owls and rabbits: predation against substandard individuals of an easy prey

The interactions among the multiple factors regulating predator-prey relationships make predation a more complex process than previously thought. The degree to which substandard individuals are captured disproportionately seems to be better a function of the difficulty of prey capture than of the hunting techniques (coursing vs. ambushing predators). That is, when the capture and killing of a prey species is easy, substandard individuals will be predated in proportion to their occurrence in the prey population. In the present study, we made use of eagle owls Bubo bubo and their main prey, the rabbit Oryctolagus cuniculus: (a) the brightness of the white tails of rabbits seems to be correlated with the physical condition of individuals, (b) by using the tails of predated rabbits as an index of individual condition, we found that eagle owls seem to prefer substandard individuals (characterized by duller tails), and (c) by using information from continuous radiotracking of 14 individuals, we suggest that the difficulty of rabbit capture could be low. Although the relative benefits of preying on substandard individuals should considerably decrease when a predator is attacking an easy prey, we hypothesise that the eagle owl preference for substandard individuals could be due to the easy detection of poor individuals by a visual cue, the brightness of the rabbit tail. Several elements allow us to believe that this form of visual communication between a prey and one of its main predators could be more widespread than previously thought. In fact: (a) visual signalling plays a relevant role in intraspecific communication in eagle owls and, consequently, visual signals could also play a role in interspecific interactions, and (b) empirical studies showed that signals may inform the predator that it has been perceived, or that the prey is in a sufficiently healthy state to elude the predator.

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history

Greek speakers say "ovpa", Germans "schwanz'' and the French "queue'' to describe what English speakers call a 'tail', but all of these languages use a related form of 'two' to describe the number after one. Among more than 100 Indo-European languages and dialects, the words for some meanings (such as 'tail') evolve rapidly, being expressed across languages by dozens of unrelated words, while others evolve much more slowly-such as the number 'two', for which all Indo-European language speakers use the same related word-form(1). No general linguistic mechanism has been advanced to explain this striking variation in rates of lexical replacement among meanings. Here we use four large and divergent language corpora (English(2), Spanish(3), Russian(4) and Greek(5)) and a comparative database of 200 fundamental vocabulary meanings in 87 Indo-European languages(6) to show that the frequency with which these words are used in modern language predicts their rate of replacement over thousands of years of Indo-European language evolution. Across all 200 meanings, frequently used words evolve at slower rates and infrequently used words evolve more rapidly. This relationship holds separately and identically across parts of speech for each of the four language corpora, and accounts for approximately 50% of the variation in historical rates of lexical replacement. We propose that the frequency with which specific words are used in everyday language exerts a general and law-like influence on their rates of evolution. Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages.

Lymph heart in chick - somitic origin, development and embryonic oedema

The lymph heart is a sac-like structure on either side of avian tail. In some adult birds, it empties the lymph from the copulatory organ; however, during embryonic development, it is thought to circulate extra-embryonic lymph. Very little is known about the origin, innervation and the cellular changes it undergoes during development. Using immunohistochemistry and gene expression profiling we show that the musculature of the lymph heart is initially composed solely of striated skeletal muscle but later develops an additional layer composed of smooth myofibroblasts. Chick-quail fate-mapping demonstrates that the lymph heart originates from the hypaxial compartments of somites 34-41. The embryonic lymph heart is transiently innervated by somatic motoneurons with no autonomic input. In comparison to body muscles, the lymph heart has different sensitivity to neuromuscular junction blockers (sensitive only to decamethonium). Furthermore, its abundant bungarotoxin-positive acetylcholinesterase receptors are unique as they completely lack specific acetylcholinesterase activity. Several lines of evidence suggest that the lymph heart may possess an intrinsic pacing mechanism. Finally, we assessed the function of the lymph heart during embryogenesis and demonstrate that it is responsible for preventing embryonic oedema in birds, a role previously thought to be played by body skeletal muscle contractions.

Platelet PECAM-1 inhibits thrombus formation in vivo

Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a cell surface glycoprotein receptor expressed on a range of blood cells, including platelets, and on vascular endothelial cells. PECAM-1 possesses adhesive and signaling properties, the latter being mediated by immunoreceptor tyrosine-based inhibitory motifs present on the cytoplasmic tail of the protein. Recent studies in vitro have demonstrated that PECAM-1 signaling inhibits the aggregation of platelets. In the present study we have used PECAM-1-deficient mice and radiation chimeras to investigate the function of this receptor in the regulation of thrombus formation. Using intravital microscopy and laser-induced injury to cremaster muscle arterioles, we show that thrombi formed in PECAM-1-deficient mice were larger, formed more rapidly than in control mice, and were more stable. Larger thrombi were also formed in control mice that received transplants of PECAM-1-deficient bone marrow, in comparison to mice that received control transplants. A ferric chloride model of thrombosis was used to investigate thrombus formation in carotid arteries. In PECAM-1-deficient mice the time to 75% vessel occlusion was significantly shorter than in control mice. These data provide evidence for the involvement of platelet PECAM-1 in the negative regulation of thrombus formation.

Factors required for the uridylylation of the foot-and-mouth disease virus 3B1, 3B2, and 3B3 peptides by the RNA-dependent RNA polymerase (3D(pol)) in vitro

The 5' terminus of picornavirus genomic RNA is covalently linked to the virus-encoded peptide 313 (VTg). Foot-and-mouth disease virus (FMDV) is unique in encoding and using 3 distinct forms of this peptide. These peptides each act as primers for RNA synthesis by the virus-encoded RNA polymerase 3D(pol). To act as the primer for positive-strand RNA synthesis, the 3B peptides have to be uridylylated to form VPgpU(pU). For certain picornaviruses, it has been shown that this reaction is achieved by the 3D(pol) in the presence of the 3CD precursor plus an internal RNA sequence termed a cis-acting replication element (cre). The FMDV ere has been identified previously to be within the 5' untranslated region, whereas all other picornavirus cre structures are within the viral coding region. The requirements for the in vitro uridylylation of each of the FMDV 313 peptides has now been determined, and the role of the FMDV ere (also known as the 3B-uridylylation site, or bus) in this reaction has been analyzed. The poly(A) tail does not act as a significant template for FMDV 3B uridylylation.

The poliovirus 2C cis-acting replication element-mediated uridylylation of VPg is not required for synthesis of negative-sense genomes

Nucleotides in the terminal loop of the poliovirus 2C cis-acting replication element (2C(CRE)), a 61 nt structured RNA, function as the template for the addition of two uridylate (U) residues to the viral protein VPg. This uridylylation reaction leads to the formation of VPgpUpU, which is used by the viral RNA polymerase as a nucleotide-peptide primer for genome replication. Although VPg primes both positive- and negative-strand replication, the specific requirement for 2C(CRE)-mediated uridylylation for one or both events has not been demonstrated. We have used a cell-free in vitro translation and replication reaction to demonstrate that 2C(CRE) is not required for the initiation of the negative-sense strand, which is synthesized in the absence of 2C(CRE)-mediated VPgpUpU formation. We propose that the 3' poly(A) tail could serve as the template for the formation of a VPg-poly(U) primer that functions in the initiation of negative-sense strands.

Synthesis and structure-activity relationship studies of CD4 down-modulating cyclotriazadisulfonamide (CADA) analogues

HIV attachment via the CD4 receptor is an important target for developing novel approaches to HIV chemotherapy. Cyclotriazadisulfonamide (CADA) inhibits HIV at submicromolar levels by specifically down-modulating cell-surface and intracellular CD4. An effective five-step synthesis of CADA in 30% overall yield is reported. This synthesis has also been modified to produce more than 50 analogues. Many tail-group analogues have been made by removing the benzyl tail of CADA and replacing it with various alkyl, acyl, alkoxycarbonyl and aminocarbonyl substituents. A series of sidearm analogues, including two unsymmetrical compounds, have also been prepared by modifying the CADA synthesis, replacing the toluenesulfonyl sidearms with other sulfonyl groups. Testing 30 of these compounds in MT-4 cells shows a wide range of CD4 down-modulation potency, which correlates with ability to inhibit HIV-1. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. The X-ray crystal structures of four compounds, including CADA, show the same major conformation of the central 12-membered ring. The solid-state structure of CADA was energy minimized and used to generate the remaining 29 structures, which were similarly minimized and aligned to produce the 3D-QSAR models. Both models indicate that steric bulk of the tail group, and, to a lesser extent, the sidearms mainly determine CD4 down-modulation potency in this series of compounds.

Dicaesium pentacyanotricuprate(I), Cs2Cu3(CN)(5)

Cs2Cu3(CN)(5) has a layered structure consisting of [Cu-3(CN)(5)](2-) sheets stacked in an ABAB fashion along the c axis, with Cs+ cations lying between the sheets. The sheets are generated by linking -(CuCN) - chains, in which the C N groups are ordered, via [Cu(CN)(3)](2-) units. The two bridging cyanide groups of each [Cu(CN)(3)](2-) unit show partial 'head-to-tail' disorder of C and N, whilst the third C N group is terminal and ordered with C bonded to Cu.

Conformational and self-assembly studies of helix forming hexapeptides containing two alpha-amino isobutyric acids

Single crystal X-ray diffraction studies reveal that three hexapeptides with general formula Boc-Ile-Aib-Xx-Ile-Aib-Yy-OMe, where Xx and Yy are Leu in peptide I, Len and Phe in peptide II, and Phe and Leu in peptide III, respectively, adopt equivalent conformations that can be described as mixed 3(10)/alpha-helice with two 4 -> 1 and two 5 -> 1 intramolecular N-H center dot center dot center dot O=C H-bonds. The peptides do not generate any helixterminating Schellman motif despite having Aib at the penultimate position from C-terminus. In the crystalline state, the helices are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. The CD Studies of the three hexapeptides in acetonitrile indicate that they are folded in well-developed 3(10)-helical structures. NMR studies of peptide I in CDCl3 also suggest the formation of a homogeneous 3 m-helical structure. The field emission scanning electron microscopic (FE-SEM) images of peptide 11 in the solid state reveal a non-twisted ribbon-like morphology, which is formed through lateral association of non-twisted filaments. (c) 2007 Elsevier Ltd. All rights reserved.

Overlapping double turn conformations adopted by tetrapeptides containing non-coded alpha-Amino Isobutyric Acid (AIB) and formation of tape-like structures through supramolecular helix mediated self-assembly

Single crystal X-ray diffraction studies and solvent dependent H-1 NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L- amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4 -> 1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning electron microscopic (FE-SEM) images of the tetrapeptides in the solid state reveal that they can form flat tape-like structures. The results establish that synthetic Aib containing supramolecular helices can form highly ordered self-aggregated amyloid plaque like human amylin.

Interactions of an anionic surfactant with poly(oxyalkylene) copolymers in aqueous solution

The interactions of sodium dodecyl sulfate (SDS) with poly(ethylene oxide)/poly(alkylene oxide) (E/A) block copolymers are explored in this study: With respect to the specific compositional characteristics of the copolymer, introduction of SDS can induce fundamentally different effects to the self-assembly behavior of E/A copolymer solutions. In the case of the E18B10-SDS system (E = poly(ethylene oxide) and B = poly(butylene oxide)) development of large surfactant-polymer aggregates was observed. In the case of B20E610-SDS, B12E227B12-SDS, E40B10E40-SDS, E19P43E19-SDS (P = poly(propylene oxide)), the formation of smaller particles compared to pure polymeric micelles points to micellar suppression induced by the ionic surfactant. This effect can be ascribed to a physical binding between the hydrophobic block of unassociated macromolecules and the non-polar tail of the surfactant. Analysis of critical micelle concentrations (cmc*) of polymer-surfactant aqueous solutions within the framework of regular solution theory for binary surfactants revealed negative deviations from ideal behavior for E40B10E40-SDS and E19P43E19-SDS, but positive deviations for E18B10-SDS. Ultrasonic studies performed for the E19P43E19-SDS system enabled the identification of three distinct regions, corresponding to three main steps of the complexation; SDS absorption to the hydrophobic backbone of polymer, development of polymer-surfactant complexes and gradual breakdown of the mixed aggregates. (C) 2008 Elsevier Inc. All rights reserved.

Influence of environmental stress on distributions of times to first division in Escherichia coli populations, as determined by digital-image analysis of individual cells

The distributions of times to first cell division were determined for populations of Escherichia coli stationary-phase cells inoculated onto agar media. This was accomplished by using automated analysis of digital images of individual cells growing on agar and calculation of the "box area ratio." Using approximately 300 cells per experiment, the mean time to first division and standard deviation for cells grown in liquid medium at 37 degrees C and inoculated on agar and incubated at 20 degrees C were determined as 3.0 h and 0.7 h, respectively. Distributions were observed to tail toward the higher values, but no definitive model distribution was identified. Both preinoculation stress by heating cultures at 50 degrees C and postinoculation stress by growth in the presence of higher concentrations of NaCl increased mean times to first division. Both stresses also resulted in an increase in the spread of the distributions that was proportional to the mean division time, the coefficient of variation being constant at approximately 0.2 in all cases. The "relative division time," which is the time to first division for individual cells expressed in terms of the cell size doubling time, was used as measure of the "work to be done" to prepare for cell division. Relative division times were greater for heat-stressed cells than for those growing under osmotic stress.

New mathematical modeling approach for predicting microbial inactivation by high hydrostatic pressure

A new primary model based on a thermodynamically consistent first-order kinetic approach was constructed to describe non-log-linear inactivation kinetics of pressure-treated bacteria. The model assumes a first-order process in which the specific inactivation rate changes inversely with the square root of time. The model gave reasonable fits to experimental data over six to seven orders of magnitude. It was also tested on 138 published data sets and provided good fits in about 70% of cases in which the shape of the curve followed the typical convex upward form. In the remainder of published examples, curves contained additional shoulder regions or extended tail regions. Curves with shoulders could be accommodated by including an additional time delay parameter and curves with tails shoulders could be accommodated by omitting points in the tail beyond the point at which survival levels remained more or less constant. The model parameters varied regularly with pressure, which may reflect a genuine mechanistic basis for the model. This property also allowed the calculation of (a) parameters analogous to the decimal reduction time D and z, the temperature increase needed to change the D value by a factor of 10, in thermal processing, and hence the processing conditions needed to attain a desired level of inactivation; and (b) the apparent thermodynamic volumes of activation associated with the lethal events. The hypothesis that inactivation rates changed as a function of the square root of time would be consistent with a diffusion-limited process.

Perceptual compensation for effects of echo and of reverberation on speech identification

In an ideal "reverberant" room, the energy of the impulse responses decays smoothly, at a constant rate of dB/s, so that gradually-decaying tails are added at the ends of sounds. Conversely, a single echo gives a flat energy-decay up to the echo's arrival time, which then drops abruptly, so that sounds with only echoes lack the decaying-tail feature of reverberation. The perceptual effects of these types of reflection pattern were measured with test-words from a continuum of steps between "sir" and "stir", which were each embedded in a carrier phrase. When the proportion of reflected sound in test-words is increased, to a level above the amount in the carrier, the test words sound more like "sir". However, when the proportion of reflected sound in the carrier is also increased, to match the amount in the test word, there can be a perceptual compensation where test words sound more like "stir" again. A reference condition used real-room reverberation from recordings at different source to receiver distances. In a synthetic-reverberation condition, the reflection pattern was from a "colorless" impulse response, comprising exponentially-decaying reflections that were spaced at intervals. In a synthetic-echo condition, the reflection pattern was obtained from the synthetic reverberation by removing the intervals between reflections before delaying the resulting cluster relative to the direct sound. Compensation occurred in the reference condition and in different types of synthetic reverberation, but not in synthetic-echo conditions. This result indicates that the presence of tails from reverberation informs the compensation mechanism.