bluuebunny/crossref_metadata_2025 huggingface dataset:
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
Authors: Mickler Moritz , Dima Ruxandra I. , Dietz Hendrik , Hyeon Changbong , Thirumalai D. , Rief Matthias
Published: December 2007

Nanomanipulation of biomolecules by using single-molecule methods and computer simulations has made it possible to visualize the energy landscape of biomolecules and the structures that are sampled during the folding process. We use simulations and single-molecule force spectroscopy to map the complex energy landscape of GFP that is used as a marker in cell biology and biotechnology. By engineering internal disulfide bonds at selected positions in the GFP structure, mechanical unfolding routes are precisely controlled, thus allowing us to infer features of the energy landscape of the wild-type GFP. To elucidate the structures of the unfolding pathways and reveal the multiple unfolding routes, the experimental results are complemented with simulations of a self-organized polymer (SOP) model of GFP. The SOP representation of proteins, which is a coarse-grained description of biomolecules, allows us to perform forced-induced simulations at loading rates and time scales that closely match those used in atomic force microscopy experiments. By using the combined approach, we show that forced unfolding of GFP involves a bifurcation in the pathways to the stretched state. After detachment of an N-terminal α-helix, unfolding proceeds along two distinct pathways. In the dominant pathway, unfolding starts from the detachment of the primary N-terminal β-strand, while in the minor pathway rupture of the last, C-terminal β-strand initiates the unfolding process. The combined approach has allowed us to map the features of the complex energy landscape of GFP including a characterization of the structures, albeit at a coarse-grained level, of the three metastable intermediates.
Revealing the multiple structures of serine
Authors: Blanco Susana , Sanz M. Eugenia , López Juan C. , Alonso José L.
Published: December 2007

We explored the conformational landscape of the proteinogenic amino acid serine [CH
2
OH

CH(NH
2
)

COOH] in the gas phase. Solid serine was vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. In the isolation conditions of the jet there have been discovered up to seven different neutral (non-zwitterionic) structures of serine, which are conclusively identified by the comparison between the experimental values of the rotational and quadrupole coupling constants with those predicted by
ab initio
calculations. These seven forms can serve as a basis to represent the shape of serine in the gas phase. From the postexpansion abundances we derived the conformational stability trend, which is controlled by the subtle network of intramolecular hydrogen bonds formed between the polar groups in the amino acid backbone and the hydroxy side chain. It is proposed that conformational cooling perturbs the equilibrium conformational distribution; thus, some of the lower-energy forms are “missing” in the supersonic expansion.
Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in
Arabidopsis
Authors: Tran Lam-Son Phan , Urao Takeshi , Qin Feng , Maruyama Kyonoshin , Kakimoto Tatsuo , Shinozaki Kazuo , Yamaguchi-Shinozaki Kazuko
Published: December 2007

In plants, multistep component systems play important roles in signal transduction in response to environmental stimuli and plant growth regulators.
Arabidopsis
contains six nonethylene receptor histidine kinases, and, among them,
AHK1/ATHK1
,
AHK2
,
AHK3
, and
CRE1
were shown to be stress-responsive, suggesting their roles in the regulation of plant response to abiotic stress. Gain- and loss-of-function studies in
Arabidopsis
indicated that AHK1 is a positive regulator of drought and salt stress responses and abscisic acid (ABA) signaling. Microarray analysis of the
ahk1
mutant revealed a down-regulation of many stress- and/or ABA-inducible genes, including AREB1, ANAC, and DREB2A transcription factors and their downstream genes. These data suggest that AHK1 functions upstream of AREB1, ANAC, and DREB2A and positively controls stress responses through both ABA-dependent and ABA-independent signaling pathways. In addition, AHK1 plays important roles in plant growth because the
ahk1 ahk2 ahk3
triple mutant showed further reduced growth. Unlike AHK1, loss-of-function analysis of
ahk2
,
ahk3
, and
cre1
implied that the stress-responsive AHK2, AHK3, and CRE1 act as negative regulators in ABA signaling. AHK2 and AHK3 also negatively control osmotic stress responses in
Arabidopsis
because
ahk2
,
ahk3
, and
ahk2 ahk3
mutants were strongly tolerant to drought and salt stress due to up-regulation of many stress- and/or ABA-inducible genes. Last, cytokinin clearly mediates stress responses because it was required for CRE1 to function as a negative regulator of osmotic stress.
Placental syncytins: Genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins
Authors: Mangeney Marianne , Renard Martial , Schlecht-Louf Géraldine , Bouallaga Isabelle , Heidmann Odile , Letzelter Claire , Richaud Aurélien , Ducos Bertrand , Heidmann Thierry
Published: December 2007

We have previously demonstrated that the envelope proteins of a murine and primate retrovirus are immunosuppressive
in vivo
. This property was manifested by the ability of the proteins, when expressed by allogeneic tumor cells normally rejected by engrafted mice, to have the
env
-expressing cells escape (at least transiently) immune rejection. Here, we analyzed the immunosuppressive activity of the human and murine syncytins. These are envelope genes from endogenous retroviruses independently coopted by ancestral hosts, conserved in evolution, specifically expressed in the placenta, and with a cell–cell fusogenic activity likely contributing to placenta morphogenesis. We show that in both humans and mice, one of the two syncytins (human syncytin-2 and mouse syncytin-B) is immunosuppressive and, rather unexpectedly, the other (human syncytin-1 and mouse syncytin-A) is not (albeit able to induce cell–cell fusion). Delineation of the immunosuppressive domain by deletion analysis, combined with a comparison between immunosuppressive and nonimmunosuppressive sequences, allowed us to derive a mutation rule targeted to specific amino acids, resulting in selective switch from immunosuppressive to nonimmunosuppressive envelope proteins and vice versa. These results unravel a critical function of retroviral envelopes, not necessarily “individually” selected for in the retrovirus endogenization process, albeit “tandemly” conserved in evolution for the syncytin pairs in primates and Muridae. Selective inactivation of immunosuppression, under conditions not affecting fusogenicity, should be important for understanding the role of this function in placental physiology and maternofetal tolerance.
Oscillations in extracellular pH and reactive oxygen species modulate tip growth of
Arabidopsis
root hairs
Authors: Monshausen G. B. , Bibikova T. N. , Messerli M. A. , Shi C. , Gilroy S.
Published: December 2007

Root hairs show highly localized cell expansion focused to their growing tips. This growth pattern is accomplished through restriction of secretion to the elongating apex and modulation of cell wall properties, with the wall just behind the tip becoming rigidified to resist the lateral expansive forces of turgor. In this report we show that root hairs exhibit oscillating growth that is associated with oscillating increases in extracellular pH and reactive oxygen species (ROS), which lag growth by ≈7 s. Consistent with a role for these changes in growth control, artificially increasing extracellular pH arrested root hair elongation, whereas decreasing pH elicited bursting at the tip. Similarly, application of exogenous ROS arrested elongation, whereas scavenging of ROS led to root hair bursting. Roots hairs of the root hair-defective
rhd2-1
mutant, which lack a functional version of the NADPH oxidase ATRBOH C, burst at the transition to tip growth. This phenotype could be rescued by elevating the pH of the growth medium to ≥6.0. Such rescued root hairs showed reduced cytoplasmic ROS levels and a lack of the oscillatory production of ROS at the tip. However, they exhibited apparently normal tip growth, including generation of the tip-focused Ca
2+
gradient thought to drive apical growth, indicating that ATRBOH C is not absolutely required to sustain tip growth. These observations indicate that root hair elongation is coupled to spatially distinct regulation of extracellular pH and ROS production that likely affect wall properties associated with the polarized expansion of the cell.
Energetics of neuronal signaling and fMRI activity
Authors: Maandag Natasja J. G. , Coman Daniel , Sanganahalli Basavaraju G. , Herman Peter , Smith Arien J. , Blumenfeld Hal , Shulman Robert G. , Hyder Fahmeed
Published: December 2007

Energetics of resting and evoked fMRI signals were related to localized ensemble firing rates (ν) measured by electrophysiology in rats. Two different unstimulated, or baseline, states were established by anesthesia. Halothane and α-chloralose established baseline states of high and low energy, respectively, in which forepaw stimulation excited the contralateral primary somatosensory cortex (S1). With α-chloralose, forepaw stimulation induced strong and reproducible fMRI activations in the contralateral S1, where the ensemble firing was dominated by slow signaling neurons (SSN; ν range of 1–13 Hz). Under halothane, weaker and less reproducible fMRI activations were observed in the contralateral S1 and elsewhere in the cortex, but ensemble activity in S1 was dominated by rapid signaling neurons (RSN; ν range of 13–40 Hz). For both baseline states, the RSN activity (i.e., higher frequencies, including the γ band) did not vary upon stimulation, whereas the SSN activity (i.e., α band and lower frequencies) did change. In the high energy baseline state, a large majority of total oxidative energy [cerebral metabolic rate of oxygen consumption (CMRO2)] was devoted to RSN activity, whereas in the low energy baseline state, it was roughly divided between SSN and RSN activities. We hypothesize that in the high energy baseline state, the evoked changes in fMRI activation in areas beyond S1 are supported by rich intracortical interactions represented by RSN. We discuss implications for interpreting fMRI data where stimulus-specific ΔCMRO2is generally small compared with baseline CMRO2.
Neural representations of kinematic laws of motion: Evidence for action-perception coupling
Authors: Dayan Eran , Casile Antonino , Levit-Binnun Nava , Giese Martin A. , Hendler Talma , Flash Tamar
Published: December 2007

Behavioral and modeling studies have established that curved and drawing human hand movements obey the 2/3 power law, which dictates a strong coupling between movement curvature and velocity. Human motion perception seems to reflect this constraint. The functional MRI study reported here demonstrates that the brain's response to this law of motion is much stronger and more widespread than to other types of motion. Compliance with this law is reflected in the activation of a large network of brain areas subserving motor production, visual motion processing, and action observation functions. Hence, these results strongly support the notion of similar neural coding for motion perception and production. These findings suggest that cortical motion representations are optimally tuned to the kinematic and geometrical invariants characterizing biological actions.
A chemical approach to unraveling the biological function of the glycosylphosphatidylinositol anchor
Authors: Paulick Margot G. , Forstner Martin B. , Groves Jay T. , Bertozzi Carolyn R.
Published: December 2007

The glycosylphosphatidylinositol (GPI) anchor is a C-terminal posttranslational modification found on many eukaryotic proteins that reside in the outer leaflet of the cell membrane. The complex and diverse structures of GPI anchors suggest a rich spectrum of biological functions, but few have been confirmed experimentally because of the lack of appropriate techniques that allow for structural perturbation in a cellular context. We previously synthesized a series of GPI anchor analogs with systematic deletions within the glycan core and coupled them to the GFP by a combination of expressed protein ligation and native chemical ligation [Paulick MG, Wise AR, Forstner MB, Groves JT, Bertozzi CR (2007)
J Am Chem Soc
129:11543–11550]. Here we investigate the behavior of these GPI-protein analogs in living cells. These modified proteins integrated into the plasma membranes of a variety of mammalian cells and were internalized and directed to recycling endosomes similarly to GFP bearing a native GPI anchor. The GPI-protein analogs also diffused freely in cellular membranes. However, changes in the glycan structure significantly affected membrane mobility, with the loss of monosaccharide units correlating to decreased diffusion. Thus, this cellular system provides a platform for dissecting the contributions of various GPI anchor components to their biological function.
Visualization of stress tensors determined by neutron diffraction
Authors: Yaman Mecit , Kriz Ronald D. , Härting Margit
Published: December 2007

The concepts and advantages of scientific visualization in the analysis of residual stress are demonstrated, using data obtained from neutron diffraction for a welded component. Because of the discrete nature of the data set, we have used local glyphs to image the stress tensor and its orientation relative to the sample. The traditional stress ellipsoid is the most natural and intuitive glyph which clearly shows the orientation and relative magnitudes of the principal stresses. Colour coding is necessary to convey the maximum possible information, leading to the introduction of the principle–normal–shear (PNS) glyph, in which the orientation of the stress vector is mapped as a colour onto the ellipsoid surface. This indicates, in an intuitive manner, the nature of the traction forces—tensile, compressive and shear—and their orientation in the material. This information can be used in combination with knowledge of the microstructure and loading patterns to identify potential failure modes and locations in the sample.
Comparison between single peak and Rietveld analysis of a zircaloy-4 weldment
Authors: Holden T.M. , Clausen B. , Carr D.G.
Published: December 2007

A comparison has been made between weld stresses in a Zircaloy-4 weld obtained by fitting individual peaks of the diffraction spectrum and by fitting the complete pattern by the Rietveld method. For the as-welded case there was satisfactory agreement between the two approaches. For the as-annealed case the agreement is less satisfactory possibly because of systematic errors in the “stress-free references”. It is suggested that the reference samples should have been cut from an annealed companion weld rather than by annealing the reference samples originally cut from the as-welded sample.
Munc18-1 Is Critical for Plasma Membrane Localization of Syntaxin1 but Not of SNAP-25 in PC12 Cells
Authors: Arunachalam Lakshmanan , Han Liping , Tassew Nardos G. , He Yu , Wang Li , Xie Li , Fujita Yoshihito , Kwan Edwin , Davletov Bazbek , Monnier Philippe P. , Gaisano Herbert Y. , Sugita Shuzo
Published: December 2007

Although Munc18-1 was originally identified as a syntaxin1–interacting protein, the physiological significance of this interaction remains unclear. In fact, recent studies of Munc18-1 mutants have suggested that Munc18-1 plays a critical role for docking of secretory vesicles, independent of syntaxin1 regulation. Here we investigated the role of Munc18-1 in syntaxin1 localization by generating stable neuroendocrine cell lines in which Munc18-1 was strongly down-regulated. In these cells, the secretion capability, as well as the docking of dense-core vesicles, was significantly reduced. More importantly, not only was the expression level of syntaxin1 reduced, but the localization of syntaxin1 at the plasma membrane was also severely perturbed. The mislocalized syntaxin1 resided primarily in the perinuclear region of the cells, in which it was highly colocalized with Secretogranin II, a marker protein for dense-core vesicles. In contrast, the expression level and the plasma membrane localization of SNAP-25 were not affected. Furthermore, the syntaxin1 localization and the secretion capability were restored upon transfection-mediated reintroduction of Munc18-1. Our results indicate that endogenous Munc18-1 plays a critical role for the plasma membrane localization of syntaxin1 in neuroendocrine cells and therefore necessitates the interpretation of Munc18-1 mutant phenotypes to be in terms of mislocalized syntaxin1.
Genetic Structure of Phaeosphaeria nodorum Populations in the North-Central and Midwestern United States
Authors: Adhikari T. B. , Ali S. , Burlakoti R. R. , Singh P. K. , Mergoum M. , Goodwin S. B.
Published: December 2007

Stagonospora nodorum blotch, caused by Phaeosphaeria nodorum, is considered one of the most destructive foliar diseases of wheat in the United States. However, relatively little is known about the population biology of this fungus in the major wheat-growing regions of the central United States. To rectify this situation, 308 single-spore isolates of P. nodorum were analyzed from 12 populations, five from hard red spring wheat cultivars in Minnesota and North Dakota and seven from soft red winter wheat in Indiana and Ohio. The genetic structure of the sampled populations was determined by analyzing polymorphisms at five microsatellite or simple-sequence repeat (SSR) loci and the mating type locus. Although a few clones were identified, most P. nodorum populations had high levels of gene (HS = 0.175 to 0.519) and genotype (D = 0.600 to 0.972) diversity. Gene diversity was higher among isolates collected from spring wheat cultivars in North Dakota and Minnesota (mean HS = 0.503) than in those from winter wheat cultivars in Indiana and Ohio (HS = 0.269). Analyses of clone-corrected data sets showed equal frequencies of both mating types in both regional and local populations, indicating that sexual recombination may occur regularly. However, significant gametic disequilibrium occurred in three of the four populations from North Dakota, and there was genetic differentiation both within and among locations. Genetic differentiation between the hard red spring and soft red winter wheat production regions was moderate (FST = 0.168), but whether this is due to differences in wheat production or to geographical variation cannot be determined. These results suggest that sexual reproduction occurs in P. nodorum populations in the major wheat-growing regions of the central United States, and that geographically separated populations can be genetically differentiated, reflecting either restrictions on gene flow or selection.
Reassessment of Vegetative Compatibility of Sclerotinia homoeocarpa Using Nitrate-Nonutilizing Mutants
Authors: Jo Y.-K. , Chang S. W. , Rees J. , Jung G.
Published: December 2007

Nitrate-nonutilizing (nit) mutants were recovered for the first time from 21 isolates of Sclerotinia homoeocarpa collected in the United States. Mutants were selected from shredded mycelium of each isolate when cultured on water agar medium amended with 4% (wt/vol) potassium chlorate. The mutants could be classified into three phenotypes: nit1, nit3, and NitM, based on their growth on minimal medium (Czapek solution agar) supplemented with NaNO2 or hypoxanthine. Complementary heterokaryons were observed in pairings between different phenotypes of nit mutants derived from compatible isolates, but not in self-fusions or pairings between incompatible isolates. The vigor of prototrophic growth varied with isolates and mutant phenotypes. Strong and continuous heterokaryons, as well as weak and spontaneous ones, formed depending on pairings of nit mutants. Stable heterokaryons between compatible isolates, but apoptotic reactions between incompatible isolates, were observed immediately after hyphal fusion under the epifluorescence microscope. The 21 isolates used in this study, which were previously assigned into 11 different vegetative compatibility groups (VCGs) based on the formation of a barrage zone at the contact site of paired isolates on complete medium (potato dextrose agar), were regrouped into five VCGs based on heterokaryon formation between nit mutants on minimal medium.
Integrated diversification of locomotion and feeding in labrid fishes
Authors: Collar David C , Wainwright Peter C , Alfaro Michael E
Published: December 2007

An organism's performance of any ecological task involves coordination of multiple functional systems. Feeding performance is influenced by locomotor abilities which are used during search and capture of prey, as well as cranial mechanics, which affect prey capture and processing. But, does this integration of functional systems manifest itself during evolution? We asked whether the locomotor and feeding systems evolved in association in one of the most prominent and diverse reef fish radiations, the Labridae. We examined features of the pectoral fins that affect swimming performance and aspects of the skull that describe force and motion of the jaws. We applied a recent phylogeny, calculated independent contrasts for 60 nodes and performed principal components analyses separately on contrasts for fin and skull traits. The major axes of fin and skull diversification are highly correlated; modifications of the skull to amplify the speed of jaw movements are correlated with changes in the pectoral fins that increase swimming speed, and increases in force capacity of the skull are associated with changes towards fins that produce high thrust at slow speeds. These results indicate that the labrid radiation involved a strong connection between locomotion and feeding abilities.
Origin of tropical American burrowing reptiles by transatlantic rafting
Authors: Vidal Nicolas , Azvolinsky Anna , Cruaud Corinne , Hedges S.Blair
Published: December 2007

Populations of terrestrial or freshwater taxa that are separated by oceans can be explained by either oceanic dispersal or fragmentation of a previously contiguous land mass. Amphisbaenians, the worm lizards (approx. 165 species), are small squamate reptiles that are uniquely adapted to a burrowing lifestyle and inhabit Africa, South America, Caribbean Islands, North America, Europe and the Middle East. All but a few species are limbless and they rarely leave their subterranean burrows. Given their peculiar habits, the distribution of amphisbaenians has been assumed to be primarily the result of two land-mass fragmentation events: the split of the supercontinent Pangaea starting 200 Myr ago, separating species on the northern land mass (Laurasia) from those on the southern land mass (Gondwana), and the split of South America from Africa 100 Myr ago. Here we show with molecular evidence that oceanic dispersal—on floating islands—played a more prominent role, and that amphisbaenians crossed the Atlantic Ocean in the Eocene (40 Myr ago) resulting in a tropical American radiation representing one-half of all known amphisbaenian species. Until now, only four or five transatlantic dispersal events were known in terrestrial vertebrates. Significantly, this is the first such dispersal event to involve a group that burrows, an unexpected lifestyle for an oceanic disperser.
Design principles for phase-splitting behaviour of coupled cellular oscillators: clues from hamsters with ‘split’ circadian rhythms
Authors: Indic Premananda , Schwartz William J , Paydarfar David
Published: December 2007

Nonlinear interactions among coupled cellular oscillators are likely to underlie a variety of complex rhythmic behaviours. Here we consider the case of one such behaviour, a doubling of rhythm frequency caused by the spontaneous splitting of a population of synchronized oscillators into two subgroups each oscillating in anti-phase (
phase-splitting
). An example of biological phase-splitting is the frequency doubling of the circadian locomotor rhythm in hamsters housed in constant light, in which the pacemaker in the suprachiasmatic nucleus (SCN) is reconfigured with its left and right halves oscillating in anti-phase. We apply the theory of coupled phase oscillators to show that stable phase-splitting requires the presence of negative coupling terms, through delayed and/or inhibitory interactions. We also find that the inclusion of real biological constraints (that the SCN contains a finite number of non-identical noisy oscillators) implies the existence of an underlying non-uniform network architecture, in which the population of oscillators must interact through at least two types of connections. We propose that a key design principle for the frequency doubling of a population of biological oscillators is inhomogeneity of oscillator coupling.
Selective activation of mechanosensitive ion channels using magnetic particles
Authors: Hughes Steven , McBain Stuart , Dobson Jon , El Haj Alicia J
Published: December 2007

This study reports the preliminary development of a novel magnetic particle-based technique that permits the application of highly localized mechanical forces directly to specific regions of an ion-channel structure. We demonstrate that this approach can be used to directly and selectively activate a mechanosensitive ion channel of interest, namely TREK-1. It is shown that manipulation of particles targeted against the extended extracellular loop region of TREK-1 leads to changes in whole-cell currents consistent with changes in TREK-1 activity. Responses were absent when particles were coated with RGD (Arg–Gly–Asp) peptide or when magnetic fields were applied in the absence of magnetic particles. It is concluded that changes in whole-cell current are the result of direct force application to the extracellular loop region of TREK-1 and thus these results implicate this region of the channel structure in mechano-gating. It is hypothesized that the extended loop region of TREK-1 may act as a tension spring that acts to regulate sensitivity to mechanical forces, in a nature similar to that described for MscL. The development of a technique that permits the direct manipulation of mechanosensitive ion channels in real time without the need for pharmacological drugs has huge potential benefits not only for basic biological research of ion-channel gating mechanisms, but also potentially as a tool for the treatment of human diseases caused by ion-channel dysfunction.
Dispersal without errors: symmetrical ears tune into the right frequency for survival
Authors: Gagliano Monica , Depczynski Martial , Simpson Stephen D , Moore James A.Y
Published: December 2007

Vertebrate animals localize sounds by comparing differences in the acoustic signal between the two ears and, accordingly, ear structures such as the otoliths of fishes are expected to develop symmetrically. Sound recently emerged as a leading candidate cue for reef fish larvae navigating from open waters back to the reef. Clearly, the integrity of the auditory organ has a direct bearing on what and how fish larvae hear. Yet, the link between otolith symmetry and effective navigation has never been investigated in fishes. We tested whether otolith asymmetry influenced the ability of returning larvae to detect and successfully recruit to favourable reef habitats. Our results suggest that larvae with asymmetrical otoliths not only encountered greater difficulties in detecting suitable settlement habitats, but may also suffer significantly higher rates of mortality. Further, we found that otolith asymmetries arising early in the embryonic stage were not corrected by any compensational growth mechanism during the larval stage. Because these errors persist and phenotypic selection penalizes asymmetrical individuals, asymmetry is likely to play an important role in shaping wild fish populations.
Oncogene addiction: setting the stage for molecularly targeted cancer therapy
Authors: Sharma Sreenath V. , Settleman Jeffrey
Published: December 2007

In pugilistic parlance, the one-two punch is a devastating combination of blows, with the first punch setting the stage and the second delivering the knock-out. This analogy can be extended to molecularly targeted cancer therapies, with oncogene addiction serving to set the stage for tumor cell killing by a targeted therapeutic agent. While in vitro and in vivo examples abound documenting the existence of this phenomenon, the mechanistic underpinnings that govern oncogene addiction are just beginning to emerge. Our current inability to fully exploit this weakness of cancer cells stems from an incomplete understanding of oncogene addiction, which nonetheless represents one of the rare chinks in the formidable armor of cancer cells.
Long-range action of Nodal requires interaction with GDF1
Authors: Tanaka Chinatsu , Sakuma Rui , Nakamura Tetsuya , Hamada Hiroshi , Saijoh Yukio
Published: December 2007

GDF1 (growth/differentiation factor 1), a Vg1-related member of the transforming growth factor-β superfamily, is required for left–right patterning in the mouse, but the precise function of GDF1 has remained largely unknown. In contrast to previous observations, we now show that GDF1 itself is not an effective ligand but rather functions as a coligand for Nodal. GDF1 directly interacts with Nodal and thereby greatly increases its specific activity. Gdf1 expression in the node was found necessary and sufficient for initiation of asymmetric Nodal expression in the lateral plate of mouse embryos. Coexpression of GDF1 with Nodal in frog embryos increased the range of the Nodal signal. Introduction of Nodal alone into the lateral plate of Gdf1 knockout mouse embryos did not induce Lefty1 expression at the midline, whereas introduction of both Nodal and GDF1 did, showing that GDF1 is required for long-range Nodal signaling from the lateral plate to the midline. These results suggest that GDF1 regulates the activity and signaling range of Nodal through direct interaction.
Mismatch repair-dependent processing of methylation damage gives rise to persistent single-stranded gaps in newly replicated DNA
Authors: Mojas Nina , Lopes Massimo , Jiricny Josef
Published: December 2007

O6-Methylguanine (MeG) is a highly cytotoxic DNA modification generated by SN1-type methylating agents. Despite numerous studies implicating DNA replication, mismatch repair (MMR), and homologous recombination (HR) in MeG toxicity, its mode of action has remained elusive. We studied the molecular transactions in the DNA of yeast and mammalian cells treated with N-methyl-N′-nitro-N-nitrosoguanidine (MNNG). Although replication fork progression was unaffected in the first cell cycle after treatment, electron microscopic analysis revealed an accumulation of MeG- and MMR-dependent single-stranded DNA (ssDNA) gaps in newly replicated DNA. Progression into the second cell cycle required HR, while the following G2 arrest required the continued presence of MeG. Yeast cells overcame this block, while mammalian cells generally failed to recover, and those that did contained multiple sister chromatid exchanges. Notably, the arrest could be abolished by removal of MeG after the first S phase. These new data provide compelling support for the hypothesis that MMR attempts to correct MeG/C or MeG/T mispairs arising during replication. Due to the persistence of MeG in the exposed template strand, repair synthesis cannot take place, which leaves single-stranded gaps behind the replication fork. During the subsequent S phase, these gaps cause replication fork collapse and elicit recombination and cell cycle arrest.
Outsourcing, offshoring and productivity measurement in United States manufacturing
Authors: HOUSEMAN Susan
Published: December 2007

Productivity growth in a sector or economy is the economic basis for improvements in workers' wages. Recent growth of domestic and foreign outsourcing in developed economies greatly complicates the measurement and interpretation of this key economic indicator and may result in inflated and misleading increases in productivity statistics. In the context of United States manufacturing, this article points to several pieces of evidence that suggest these effects of outsourcing and offshoring on productivity measures are significant. These factors may help explain why wage growth for most United States workers has been relatively low in spite of high measured productivity growth.
Target‐cell‐dependent plasticity within the mossy fibre–CA3 circuit reveals compartmentalized regulation of presynaptic function at divergent release sites
Authors: Pelkey Kenneth A. , McBain Chris J.
Published: December 2007

Individual axons of central neurons innervate a large number of distinct postsynaptic targets belonging to divergent functional categories such as glutamatergic principal cells and inhibitory interneurons. While each bouton along a common axon should experience the same activity pattern in response to action potential firing within the parent presynaptic neuron, accumulating evidence suggests that neighbouring boutons contacting functionally distinct postsynaptic targets regulate their release properties independently, despite being separated by only a few microns. This target‐cell‐specific autonomy of presynaptic function can greatly expand the computational prowess of central axons to allow for precise coordination of large neuronal ensembles within a given circuit. An excellent example of target‐cell‐specific presynaptic mechanisms occurs in the CA3 hippocampus where mossy fibre (MF) axons of dentate gyrus granule cells target both principal cells and local circuit inhibitory interneurons via both anatomically and functionally specialized terminals. Of particular interest, mechanisms of both short‐ and long‐term plasticity remain autonomous at these divergent release sites due to an anatomical and biochemical segregation of discrete molecular signalling cascades. Here we review roughly a decades worth of research on the MF–CA3 pathway to showcase the target‐cell dependence of presynaptically expressed NMDA receptor‐independent synaptic plasticity.
Carnivorous Fungi from Cretaceous Amber
Authors: Schmidt Alexander R. , Dörfelt Heinrich , Perrichot Vincent
Published: December 2007

Carnivorous fungi dating back to the age of the dinosaurs have been found fossilized in circa-100-million-year-old amber. The fossil fungi used hyphal rings as trapping devices and are preserved together with their prey, small nematodes. The excellent preservation in amber allowed comparison with extant groups: On the basis of the mode of ring formation and the dimorphic mode of life, the fossils cannot be assigned to any recent carnivorous fungus, providing evidence that different groups occupied this ecological niche in the Cretaceous and that trapping devices were developed independently multiple times in the course of Earth history.
A 3-Hydroxypropionate/4-Hydroxybutyrate Autotrophic Carbon Dioxide Assimilation Pathway in Archaea
Authors: Berg Ivan A. , Kockelkorn Daniel , Buckel Wolfgang , Fuchs Georg
Published: December 2007

The assimilation of carbon dioxide (CO
2
) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales,
Metallosphaera sedula
, fixed CO
2
with acetyl–coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in
Metallosphaera
but also in
Sulfolobus, Archaeoglobus
, and
Cenarchaeum
species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO
2
-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.
Activity of CeO

x

and TiO

x

Nanoparticles Grown on Au(111) in the Water-Gas Shift Reaction
Authors: Rodriguez J. A. , Ma S. , Liu P. , Hrbek J. , Evans J. , Pérez M.
Published: December 2007

The high performance of Au-CeO
2
and Au-TiO
2
catalysts in the water-gas shift (WGS) reaction (H
2
O + CO→H
2
+ CO
2
) relies heavily on the direct participation of the oxide in the catalytic process. Although clean Au(111) is not catalytically active for the WGS, gold surfaces that are 20 to 30% covered by ceria or titania nanoparticles have activities comparable to those of good WGS catalysts such as Cu(111) or Cu(100). In TiO

2-
x

/Au(111) and CeO

2-
x

/Au(111), water dissociates on O vacancies of the oxide nanoparticles, CO adsorbs on Au sites located nearby, and subsequent reaction steps take place at the metal-oxide interface. In these inverse catalysts, the moderate chemical activity of bulk gold is coupled to that of a more reactive oxide.
Life in the Really Hard Places
Authors: Schmidt Tom
Published: December 2007

The Third Domain
. The Untold Story of Archaea and the Future of Biotechnology.
By Tim Friend
. Joseph Henry Press, Washington, DC, 2007. 312 pp. $27.95, C$32.95. ISBN 9780309102377.

Although the author centers his account on the work of Carl Woese, he spends much of his time describing the distribution, ecology, and potential biotech applications of the Archaea.
The
Physcomitrella
Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
Authors: Rensing Stefan A. , Lang Daniel , Zimmer Andreas D. , Terry Astrid , Salamov Asaf , Shapiro Harris , Nishiyama Tomoaki , Perroud Pierre-François , Lindquist Erika A. , Kamisugi Yasuko , Tanahashi Takako , Sakakibara Keiko , Fujita Tomomichi , Oishi Kazuko , Shin-I Tadasu , Kuroki Yoko , Toyoda Atsushi , Suzuki Yutaka , Hashimoto Shin-ichi , Yamaguchi Kazuo , Sugano Sumio , Kohara Yuji , Fujiyama Asao , Anterola Aldwin , Aoki Setsuyuki , Ashton Neil , Barbazuk W. Brad , Barker Elizabeth , Bennetzen Jeffrey L. , Blankenship Robert , Cho Sung Hyun , Dutcher Susan K. , Estelle Mark , Fawcett Jeffrey A. , Gundlach Heidrun , Hanada Kousuke , Heyl Alexander , Hicks Karen A. , Hughes Jon , Lohr Martin , Mayer Klaus , Melkozernov Alexander , Murata Takashi , Nelson David R. , Pils Birgit , Prigge Michael , Reiss Bernd , Renner Tanya , Rombauts Stephane , Rushton Paul J. , Sanderfoot Anton , Schween Gabriele , Shiu Shin-Han , Stueber Kurt , Theodoulou Frederica L. , Tu Hank , Van de Peer Yves , Verrier Paul J. , Waters Elizabeth , Wood Andrew , Yang Lixing , Cove David , Cuming Andrew C. , Hasebe Mitsuyasu , Lucas Susan , Mishler Brent D. , Reski Ralf , Grigoriev Igor V. , Quatrano Ralph S. , Boore Jeffrey L.
Published: December 2007

We report the draft genome sequence of the model moss
Physcomitrella patens
and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The
Physcomitrella
genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
Why People Turn to Bombs
Authors: Bueno de Mesquita Ethan
Published: December 2007

What Makes a Terrorist
. Economics and the Roots of Terrorism.
By Alan B. Krueger
. Princeton University Press, Princeton, NJ, 2007. 192 pp. $24.95, £14.95. ISBN 9780691134383.

The author argues that terrorists are not drawn from the desperately poor but come from better-educated and well-off classes and wish to effect social and political change.
Preparation of Bacterial DNA Template by Boiling and Effect of Immunoglobulin G as an Inhibitor in Real-Time PCR for Serum Samples from Patients with Brucellosis
Authors: Queipo-Ortuño Maria Isabel , De Dios Colmenero Juan , Macias Manuel , Bravo Maria Jose , Morata Pilar
Published: December 2007

Real-time PCR is a widely used tool for the diagnosis of many infectious diseases. However, little information exists about the influences of the different factors involved in PCR on the amplification efficiency. The aim of this study was to analyze the effect of boiling as the DNA preparation method on the efficiency of the amplification process of real-time PCR for the diagnosis of human brucellosis with serum samples. Serum samples from 10 brucellosis patients were analyzed by a SYBR green I LightCycler-based real-time PCR and by using boiling to obtain the DNA. DNA prepared by boiling lysis of the bacteria isolated from serum did not prevent the presence of inhibitors, such as immunoglobulin G (IgG), which were extracted with the template DNA. To identify and confirm the presence of IgG, serum was precipitated to separate and concentrate the IgG and was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. The use of serum volumes above 0.6 ml completely inhibited the amplification process. The inhibitory effect of IgG in serum samples was not concentration dependent, and it could be eliminated by diluting the samples 1/10 and 1/20 in water. Despite the lack of the complete elimination of the IgG from the template DNA, boiling does not require any special equipment and it provides a rapid, reproducible, and cost-effective method for the preparation of DNA from serum samples for the diagnosis of brucellosis.
Impact of Protein Shedding on Detection of
Mycobacterium avium
subsp.
paratuberculosis
by a Whole-Cell Immunoassay Incorporating Surface-Enhanced Raman Scattering
Authors: Yakes Betsy Jean , Lipert Robert J. , Bannantine John P. , Porter Marc D.
Published: December 2007

The etiological agent of Johne's disease is
Mycobacterium avium
subsp.
paratuberculosis
. Controlling the spread of this disease is hindered by the lack of sensitive, selective, and rapid detection methods for
M. avium
subsp.
paratuberculosis
. By using a recently optimized sandwich immunoassay (B. J. Yakes, R. J. Lipert, J. P. Bannantine, and M. D. Porter, Clin. Vaccine Immunol. 15:227-234, 2008), which incorporates a new monoclonal antibody for the selective capture and labeling of
M. avium
subsp.
paratuberculosis
and surface-enhanced Raman scattering for sensitive readout, detection limits of ∼630 and ∼740
M. avium
subsp.
paratuberculosis
cells/ml are achieved in phosphate-buffered saline and whole milk samples, respectively, after spiking with heat-treated
M. avium
subsp.
paratuberculosis
. Surprisingly, these detection limits are 3 orders of magnitude lower than expected based on theoretical predictions. Experiments designed to determine the origin of the improvement revealed that the major membrane protein targeted by the monoclonal antibody was present in the sample suspensions as shed protein. This finding indicates that the capture and labeling of shed protein function as a facile amplification strategy for lowering the limit of detection for
M. avium
subsp.
paratuberculosis
that may also be applicable to the design of a wide range of highly sensitive assays for other cells and viruses.
Efficient Identification of Clinically Relevant
Candida
Yeast Species by Use of an Assay Combining Panfungal Loop-Mediated Isothermal DNA Amplification with Hybridization to Species-Specific Oligonucleotide Probes
Authors: Inácio João , Flores Orfeu , Spencer-Martins Isabel
Published: December 2007

The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus
Candida
remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.
Prevalence and Characterization of Multidrug-Resistant (Type ACSSuT)
Salmonella enterica
Serovar Typhimurium Strains in Isolates from Four Gosling Farms and a Hatchery Farm
Authors: Yu Chang-You , Chou Shih-Jen , Yeh Chia-Ming , Chao Maw-Rong , Huang Kwo-Ching , Chang Yung-Fu , Chiou Chien-Shun , Weill Francois-Xavier , Chiu Cheng-Hsun , Chu Chi-Hong , Chu Chishih
Published: December 2007

Salmonella enterica
serovar Typhimurium strains of phage types DT104 and U302 are often resistant to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (the ACSSuT resistance type) and are major zoonotic pathogens. Increased consumption of goose meat may enhance the risk of transferring
S. enterica
serovar Typhimurium and other enteric pathogens from geese to human due to the consumption of meats from infected geese or improper preparation of meats. Therefore, we characterized
S. enterica
serovar Typhimurium strains isolated from four goose farms (farms A, B, C, and D) and one hatchery farm (farm E) to determine the epidemic and genetic differences among them. Antibiotic susceptibility tests and multiplex PCR confirmed that 77.6% (52/67) of strains were ACSSuT strains isolated from farms A, C, and E. Antibiotic-susceptible strains were isolated mostly from farm B, and no strain was observed in farm D. All ACSSuT strains harbored a 94.7-kb virulence plasmid and contained one 1.1-kb conserved segment identical to that of
Salmonella
genomic island 1. Four genotypes were determined among these
S. enterica
serovar Typhimurium isolates by pulsed-field gel electrophoresis analysis of XbaI-digested DNA fragments. Most isolates (85.29%; 29/34) of major genotype Ib were ACSSuT strains isolated mainly from goslings of farm C and egg membranes of farm E, a hatchery farm, suggesting that
S. enterica
serovar Typhimurium strains in isolates from goslings might originate from its hatchery, from the egg membranes to the gosling fluff after hatching. Multiple phage types, types 8, 12, U283, DT104, and U302, were identified. In conclusion, geese were a reservoir of diverse multidrug-resistant (type ACSSuT)
S. enterica
serovar Typhimurium strains, and each farm was colonized with genetically closely related
S. enterica
serovar Typhimurium strains.
Health Care-Associated Endocarditis Caused by
Staphylococcus aureus
with Reduced Susceptibility to Vancomycin
Authors: Chi Chia-Yu , Lauderdale Tsai-Ling , Wang Shih-Min , Wu Jing-Ming , Yang Yu-Jen , Liu Ching-Chuan
Published: December 2007

Infective endocarditis (IE) caused by methicillin-resistant
Staphylococcus aureus
with reduced vancomycin susceptibility (SARV) has been reported worldwide. We report the successful treatment of a pediatric patient with SARV IE and characterization of the infecting strain. The MIC of vancomycin rose from 1.5 to 2 μg/ml, and the SARV was confirmed by population analysis.