bluuebunny/crossref_metadata_2025 huggingface dataset:
The End of Cost Allocations as We Know Them
Authors: Hodak Marc
Published: April 2005

Cost allocation issues have befuddled management around the world for over a century. And, because of “informational asymmetries” and agency conflicts between operating management and headquarters, there is no clear theoretical solution to the problem. Nevertheless, there are good reasons for allocating costs. If properly structured, transfer‐pricing schemes can serve the same purpose as a market price. By communicating useful information about the relative scarcity of resources within an organization, they can serve to balance supply and demand for the product or service being priced.

Unfortunately, most transfer‐pricing approaches, like Activity Based Costing, attempt to solve the problem by refining standard cost measures. In contrast to ABC, this article begins by recognizing that efforts to develop more precise cost allocations are bound to be frustrated by the information and incentive problems noted above. And in place of more precisely formulated measures of cost, the author proposes a process of negotiation between two parties to an exchange—a process that is reinforced by a performance measurement system that gives both parties incentives to reveal their “reservation” prices for the good or service in question. For transfers involving multiple users of a given service or products, the author recommends a transfer auction process that is also designed to make would‐be users reveal their assessments of value.
The Capital Structure Puzzle: The Evidence Revisited
Authors: Barclay Michael J. , Smith Clifford W.
Published: April 2005

Since the formulation of the M&M propositions almost 50 years ago, financial economists have been debating whether there is such a thing as an optimal capital structure—a proportion of debt to equity that maximizes shareholder value. Some finance scholars have followed M&M in arguing that both capital structure and dividend policy are largely “irrelevant” in the sense that they have no significant, predictable effects on corporate market values. Another school of thought holds that corporate financing choices reflect an attempt by corporate managers to balance the tax shields and disciplinary benefits of greater debt against the costs of financial distress. Yet another theory says that companies do not have capital structure targets, but simply follow a financial “pecking order” in which retained earnings are preferred to outside financing, and debt is preferred to equity when outside funding is required.

In reviewing the evidence that has accumulated since M&M, the authors argue that taxes, bankruptcy (and other “contracting”) costs, and information costs all appear to play an important role in corporate financing decisions. While much of the evidence is consistent with the argument that companies set target leverage ratios, there is also considerable support for the pecking order theory's contention that firms are willing to deviate widely from their targets for long periods of time. According to the authors, the key to reconciling the different theories—and thus to solving the capital structure puzzle—lies in achieving a better understanding of the relation between corporate financing stocks (the levels of debt and equity in relation to the target) and flows(or which security to issue at a particular time).
Do Managers Have Capital Structure Targets? Evidence from Corporate Spinoffs
Authors: Mehrotra Vikas , Mikkelson Wayne , Partch Megan
Published: April 2005

The two main theories of capital structure—the tradeoff theory and the pecking order theory—have opposite predictions about the expected relationship between corporate leverage and profitability. According to the tradeoff theory, companies that earn higher profits will use more debt both to shield their income from corporate taxes and to discipline corporate investment policy. In contrast, the pecking order theory predicts that more profitable companies will borrow less mainly because they have less need to borrow.

Corporate spinoffs provide a unique opportunity to investigate the influence of profitability and other asset characteristics on the design of capital structure. In their study of 98 spinoffs over the period 1979–1997, the authors began by investigating the popular argument that managers routinely assign more debt to subsidiaries than parents in order to leave the parents less encumbered—a possibility they reject after finding that the average leverage ratios of the parents and spunoff units were roughly equal. At the same time, the authors reported large differences in the leverage ratios among both parents and spun‐off units, and that the variation was explained primarily by differences in three factors: asset tangibility and the level and variability of cash operating profits. Consistent with the tradeoff theory (but not the pecking order), the study found a significantly positive correlation between a post‐spinoff company's cash profitability and its assigned debt load, as well as a negative correlation between debt and the variability of operating cash flow.
Trade, Jobs, and the Economic Outlook for 2005
Authors: Plosser Charles I.
Published: April 2005

From newspaper accounts, one might think that the U.S. economy is on the verge of collapse. But the economy performed well in 2004, with real GDP growth of 3.9%, inflation at only 2.2%, unemployment down to 5.4%, and over two million jobs added to the payrolls (performance that is the envy of America's trade partners in Europe). And much the same, perhaps with moderate increases in interest rates, is expected in 2005.

Concerns about the trade deficit in particular have given rise to familiar calls to protect U.S. industries and jobs. But job losses due to “offshoring” amount to just 1% of total job losses each year, with little effect on the growth in overall employment. Manufacturing jobs have declined, but the value of manufactured goods as a share of real GDP has remained steady because of productivity growth in the manufacturing sector. Rather than spending vast amounts of money to protect jobs that are destined to go overseas, the correct policy response is to help people retrain and find employment elsewhere.

Trade deficits arise in countries that experience either investment booms or declines in savings. Thus, trade deficits are not necessarily an indication of economic failure. Foreigners invest in America because the U.S. is still the world's largest and most productive economy. And provided that the U.S. continues to offer such investment opportunities, foreign investors' search for low‐risk assets will continue to be a major (if not the main) cause of the U.S. trade deficit.
Bookbuidling, Auctions, and the Future of the IPO Process
Authors: Wilhelm William J.
Published: April 2005

Auction theorists predict that bookbuilding, long the standard process for selling equity IPOs in the U.S., is about to give way to an Internet‐based IPO auction process that is both more efficient and more fair. The promise of auctions is that, by using an electronic platform that gives all investors the opportunity to bid on IPOs, the underpricing of IPOs and commissions to underwriters will be reduced, leading to an increase in net proceeds to issuers.

Largely missing from such arguments, however, is an appreciation of why bookbuilding has dominated U.S. practice (and continues to supplant auctions in IPOs in most countries outside the U.S) and the role of undepricing in the IPO process. Rather than canvassing all investors, bookbuilding involves eliciting expressions of interest from institutional investors, and then allocating shares mainly according to the strength of their professed interest. In contrast to auctions, which allocate shares according to a set of explicit rules, bookbuilding involves a set of implicit “rules” that provide considerable room for judgment by the underwriter. This does not mean that the rules are arbitrary or not well understood by participants, particularly after thousands of IPOs conducted over the better part of two centuries. But to manage the exchange of information between issuers and investors, and the potential conflicts of interest in representing both groups, such rules must be administered by an intermediary with a considerable stake in protecting its reputation for fair dealing. Investment banks that deal with both issuers and the investment community on a regular basis are well positioned to perform this function.

The underpricing of IPOs is best viewed not as a transfer of wealth from issuers to favored investors but rather as compensation to the large influential investors that play a major role in the price discovery process. By opening the process to all comers, auctions will discourage these large investors from bidding aggressively because less sophisticated investors will be able to “free ride” on their research and due diligence. To the extent this happens, auctions may suc ceed in reducing underpricing (in fact, they may even lead to over pricing), but they will also reduce the net proceeds for issuers.

Nevertheless, recent advances in communications technology and auction theory will undoubtedly reshape current securities underwriting practices. In particular, Internet auctions are likely to replace bookbuilding in debt IPOs and less risky equity issues (say, IPOs of LBOs). But the argument that Bookbuilding will be completely cast aside in favor of largely untested alternatives fails to appreciate a successful institutional response to major market imperfections, some of which can never be wholly eliminated. Especially in the case of risky (first‐time) equity IPOs, there will continue to be an important role for managing the information exchange between issuers and investors that is critical to the IPO process.
Autoimmune‐associated Congenital Heart Block: Treatment of the Mother With Immunoadsorption
Authors: Hickstein Heiko , Külz Thomas , Claus Renate , Stange Jan , Schmidt Reinhard
Published: April 2005

Abstract:  Autoimmune‐associated congenital heart block (CHB) is a rare complication of pregnancy in mothers with Anti‐Ro/SSA antibodies (SSA‐abs), resulting in fetal myocarditis, atrioventricular block, hydrops fetalis and/or intrauterine fetal death. As these antibodies are supposed to be directly involved in the pathogenesis of CHB, their removal should be associated with an improved clinical course. Extracorporeal immunoadsorption (IA) is the most efficient method to remove IgG‐immunoglobulins like SSA‐abs selectively. Two women with high titers of those auto‐antibodies [mothers serum 615 and 612, respectively (normal range <3.0 IU/mL)] were treated with IA two to three times per gestation week in the outpatient department of the University of Rostock. In both patients, the mean removal of IgG (65 ± 6%) to a target near 2.0 g/L after IA was successful. The SSA‐abs were reduced from mean 328 ± 138 and 247 ± 105 pre IA to 88 ± 124 and 98 ± 42 post IA, respectively. One child received a pacemaker due to the persisting atrioventricular block grade III after birth. The second was unaffected. The removal of highly elevated SSA‐antibodies by immunoadsorption is a possible treatment option in pregnant woman with high titers of those antibodies and/or a positive history of clinical complications. Further clinical studies are necessary.
Effect Over Time of Endotoxin Adsorption Therapy in Sepsis
Authors: Ueno Takuya , Sugino Michio , Nemoto Hiromu , Shoji Hisataka , Kakita Akira , Watanabe Masahiko
Published: April 2005

Abstract:  Despite the use of potent antibiotics and intensive supportive care, the mortality among patients with sepsis and Gram‐negative bacteremia remains high. In recent years, endotoxin adsorption therapy (PMX‐DHP, polymyxin‐direct hemoperfusion) has been widely used in Japan to remove endotoxin, a causative agent of sepsis. In septic patients whose clinical condition may change at any moment, the decision of when to perform blood purification in addition to conventional intensive care is a critical factor in the therapeutic strategy and prognosis. In the present study, we investigated the effect over time of PMX‐DHP in sepsis. The subjects were 16 patients with systemic inflammatory response syndrome (SIRS) who required surgical treatment including a surgical operation and drainage. The following six parameters were compared between the first and second PMX‐DHP: mean blood pressure and time‐restricted urine at four time points – at baseline and  at  6,  24  and  72 h  after  PMX‐DHP;  and  white  blood  cell count, platelet count, base excess and Septic Severity Score (SSS) at 24 and 72 h after PMX‐DHP. Mean blood pressure improved over time up to 24 h after both the first and second PMX‐DHP. Time‐restricted urine volume improved only at 6 h after the first PMX‐DHP. White blood cell count improved over time up to 24 h after both the first and second PMX‐DHP. The SSS improved at all time points studied except for 3 days after the second PMX‐DHP. We conclude that PMX‐DHP is expected to have important implications in terms of (i) correction of clinical conditions (by severity assessment); (ii) improvement of hemodynamics; (iii) possible anti‐inflammatory effect; and (iv) possible improvement of oxygen metabolism in tissues.
Mathematical Analysis of Urea Rebound in Long‐term Hemodialysis Patients
Authors: Ookawara Susumu , Suzuki Masayuki , Saitou Mikio , Tabei Kaoru
Published: April 2005

Abstract:  Quantifying hemodialysis (HD) treatment requires knowledge of the equilibrated concentrations of the post‐HD small molecule rebounds. However, measurement of the equilibrated concentrations is only possible after resting in bed after HD for at least 30 min, and this is often impractical. Therefore, we have analyzed mathematically the time course of post‐HD urea rebound, and from this, have derived a new formula for predicting its equilibrated concentration. The blood urea nitrogen (BUN) was measured at 10 time points (immediately following HD, and 0.5, 2.5, 5, 7.5, 10, 15, 20, 25, and 30 min post‐HD) in 12 anuric HD patients. The absolute change in the urea rebound (ΔeqBUN) was approximated (ΔestBUN) using the equation: ΔestBUN = b –[1‐exp ×  (–c × time (min))] + a × time (min). After the good correlation between ΔeqBUN and ΔestBUN, we compared the value of ΔeqBUN measured at 30 min (ΔeqBUN30) with that calculated (ΔestBUN30) using only four sample points (immediately following HD, and 2.5, 5 and 10 min post‐HD). Based on this result, we tried to predict post‐HD BUN at 30 min (estBUN30). This study was undertaken to determine whether estBUN30 may be representative of the equilibrated BUN (eqBUN30), and to compare with Kt/V using estBUN30 and eqBUN30. There was a significant correlation between ΔeqBUN and ΔestBUN (0.97 < r < 0.99, P < 0.001). Thus, there was a significant positive linear correlation between eqBUN30 and estBUN30 (eqBUN30: 25.7 ± 2.25 mg/dL, estBUN30: 26.3 ± 2.31 mg/dL; r2 = 0.99, P < 0.001). A Kt/V measurement was obtained with single pool model using BUN just after HD (Kt/Vsp), eqBUN30 (Kt/Veq), and estBUN30 (Kt/Vest), and with double pool model using Kt/Vsp (Kt/Vdp) and was compared with them. Though Kt/Vsp was significantly higher than Kt/Veq (1.26 ± 0.08 vs. 1.09 ± 0.07, P < 0.001), there were no differences among Kt/Veq, Kt/Vest and Kt/Vdp (Kt/Vest: 1.06 ± 0.07, Kt/Vdp: 1.10 ± 0.07) and all values were clinically acceptable. Furthermore, there was a significant positive linear correlation between Kt/Veq and Kt/Vest (r2 = 0.98, P < 0.001). In conclusion, we have devised the method to predict equilibrated BUN and calculate double pool Kt/V, which requires samples up to 10 min post‐HD.
Taurine activates excitatory non‐synaptic glycine receptors on dopamine neurones in ventral tegmental area of young rats
Authors: Wang Fushun , Xiao Cheng , Ye Jiang Hong
Published: April 2005

The physiological and pharmacological properties of taurine‐induced responses were investigated in dopaminergic (DA) neurones from the ventral tegmental area (VTA) of young rats aged 1–13 postnatal days, either in acute brain slices or acutely dissociated neurones. When whole‐cell responses were recorded from current‐clamped neurones using the gramicidin‐perforated technique, the application of taurine (0.01–30 mm) accelerated firings and induced membrane depolarization. In voltage‐clamped neurones, taurine induced a current which was antagonized by strychnine and by picrotoxin, but not by bicuculline. In addition, taurine‐induced current showed complete cross‐desensitization with glycine‐activated currents but not with γ‐aminobutyric acid (GABA)‐activated currents. Thus, taurine is a full agonist of the glycine receptors (GlyRs) in the VTA. Further studies found that taurine acted mainly on non‐synaptic GlyRs. The application of 20 μm bicuculline abolished the spontaneous inhibitory post‐synaptic currents (IPSCs) in 40/45 neurones, and 93% of the evoked IPSCs. The addition of 1 μm strychnine completely eliminated the remaining IPSCs. These results suggest that GABAergic IPSCs predominate, and that functional glycinergic synapses are present in a subset of the VTA neurones. The application of 1 μm strychnine alone induced an outward current, suggesting that these neurones were exposed to tonically released taurine/glycine. In conclusion, by activating non‐synaptic GlyRs, taurine may act as an excitatory extra‐synaptic neurotransmitter in the VTA during early development.
The nitric oxide donor sodium nitroprusside stimulates the Na+–K+ pump in isolated rabbit cardiac myocytes
Authors: William Maged , Vien Jimmy , Hamilton Elisha , Garcia Alvaro , Bundgaard Henning , Clarke Ronald J , Rasmussen Helge H.
Published: April 2005

Nitric oxide (NO) affects the membrane Na+–K+ pump in a tissue‐dependent manner. Stimulation of intrinsic pump activity, stimulation secondary to NO‐induced Na+ influx into cells or inhibition has been reported. We used the whole‐cell patch clamp technique to measure electrogenic Na+–K+ pump current (Ip) in rabbit ventricular myocytes. Myocytes were voltage clamped with wide‐tipped patch pipettes to achieve optimal perfusion of the intracellular compartment, and Ip was identified as the shift in holding current induced by 100 μm ouabain. The NO donor sodium nitroprusside (SNP) in concentrations of 1, 10, 50 or 100 μm induced a significant increase in Ip when the intracellular compartment was perfused with pipette solutions containing 10 mm Na+, a concentration near physiological levels. SNP had no effect when the pump was near‐maximally activated by 80 mm Na+ in pipette solutions. Stimulation persisted in the absence of extracellular Na+, indicating its independence of transmembrane Na+ influx. The SNP‐induced pump stimulation was abolished by inhibition of soluble guanylyl cyclase (sGC) with 1H‐[1,2,4]oxadiazole[4,3‐a]quinoxalin‐1‐one, by inhibition of protein kinase G (PKG) with KT‐5823 or by inhibition of protein phosphatase with okadaic acid. Inclusion of the non‐hydrolysable cGMP analogue 8pCPT‐cGMP, activated recombinant PKG or the sGC‐activator YC‐1 in patch pipette filling solutions reproduced the SNP‐induced pump stimulation. Pump stimulation induced by YC‐1 was dependent on the Na+ concentration but not the K+ concentration in pipette filling solutions, suggesting an altered sensitivity of the Na+–K+ pump to intracellular Na+.
Local recovery of Ca2+ release in rat ventricular myocytes
Authors: Sobie Eric A. , Song Long‐Sheng , Lederer W. J.
Published: April 2005

Excitation–contraction coupling in the heart depends on the positive feedback process of Ca2+‐induced Ca2+ release (CICR). While CICR provides for robust triggering of Ca2+ sparks, the mechanisms underlying their termination remain unknown. At present, it is unclear how a cluster of Ca2+ release channels (ryanodine receptors or RyRs) can be made to turn off when their activity is sustained by the Ca2+ release itself. We use a novel experimental approach to investigate indirectly this issue by exploring restitution of Ca2+ sparks. We exploit the fact that ryanodine can bind, nearly irreversibly, to an RyR subunit (monomer) and increase the open probability of the homotetrameric channel. By applying low concentrations of ryanodine to rat ventricular myocytes, we observe repeated activations of individual Ca2+ spark sites. Examination of these repetitive Ca2+ sparks reveals that spark amplitude recovers with a time constant of 91 ms whereas the sigmoidal recovery of triggering probability lags behind amplitude recovery by ∼80 ms. We conclude that restitution of Ca2+ sparks depends on local refilling of SR stores after depletion and may also depend on another time‐dependent process such as recovery from inactivation or a slow conformational change after rebinding of Ca2+ to SR regulatory proteins.
Estimating Duration and Intensity of Neoproterozoic Snowball Glaciations from Ir Anomalies
Authors: Bodiselitsch Bernd , Koeberl Christian , Master Sharad , Reimold Wolf U.
Published: April 2005

The Neoproterozoic glaciations supposedly ended in a supergreenhouse environment, which led to rapid melting of the ice cover and precipitation of the so-called cap carbonates. If Earth was covered with ice, then extraterrestrial material would have accumulated on and within the ice and precipitated during rapid melting at the end of the glaciation. We found iridium (Ir) anomalies at the base of cap carbonates in three drill cores from the Eastern Congo craton. Our data confirm the presence of extended global Neoproterozoic glaciations and indicate that the duration of the Marinoan glacial episode was at least 3 million, and most likely 12 million, years.
Antigen Recognition Determinants of γδ T Cell Receptors
Authors: Shin Sunny , El-Diwany Ramy , Schaffert Steven , Adams Erin J. , Garcia K. Christopher , Pereira Pablo , Chien Yueh-hsiu
Published: April 2005

The molecular basis of γδ T cell receptor (TCR) recognition is poorly understood. Here, we analyze the TCR sequences of a natural γδ T cell population specific for the major histocompatibility complex class Ib molecule T22. We find that T22 recognition correlates strongly with a somatically recombined TCRδ complementarity-determining region 3 (CDR3) motif derived from germ line–encoded residues. Sequence diversity around these residues modulates TCR ligand-binding affinities, whereas V gene usage correlates mainly with tissue origin. These results show how an antigen-specific γδ TCR repertoire can be generated at a high frequency and suggest that γδ T cells recognize a limited number of antigens.
A Generalized Approach to the Modification of Solid Surfaces
Authors: Ryu Du Yeol , Shin Kyusoon , Drockenmuller Eric , Hawker Craig J. , Russell Thomas P.
Published: April 2005

Interfacial interactions underpin phenomena ranging from adhesion to surface wetting. Here, we describe a simple, rapid, and robust approach to modifying solid surfaces, based on an ultrathin cross-linkable film of a random copolymer, which does not rely on specific surface chemistries. Specifically, thin films of benzocyclobutene-functionalized random copolymers of styrene and methyl methacrylate were spin coated or transferred, then thermally cross-linked on a wide variety of metal, metal oxide, semiconductor, and polymeric surfaces, producing a coating with a controlled thickness and well-defined surface energy. The process described can be easily implemented and adapted to other systems.
A Hydrogen-Rich Early Earth Atmosphere
Authors: Tian Feng , Toon Owen B. , Pavlov Alexander A. , De Sterck H.
Published: April 2005

We show that the escape of hydrogen from early Earth's atmosphere likely occurred at rates slower by two orders of magnitude than previously thought. The balance between slow hydrogen escape and volcanic outgassing could have maintained a hydrogen mixing ratio of more than 30%. The production of prebiotic organic compounds in such an atmosphere would have been more efficient than either exogenous delivery or synthesis in hydrothermal systems. The organic soup in the oceans and ponds on early Earth would have been a more favorable place for the origin of life than previously thought.
Assortative Mating in Sympatric Host Races of the European Corn Borer
Authors: Malausa Thibaut , Bethenod Marie-Thérèse , Bontemps Arnaud , Bourguet Denis , Cornuet Jean-Marie , Ponsard Sergine
Published: April 2005

Although a growing body of work supports the plausibility of sympatric speciation in animals, the practical difficulties of directly quantifying reproductive isolation between diverging taxa remain an obstacle to analyzing this process. We used a combination of genetic and biogeochemical markers to produce a direct field estimate of assortative mating in phytophagous insect populations. We show that individuals of the same insect species, the European corn borer
Ostrinia nubilalis
, that develop on different host plants can display almost absolute reproductive isolation—the proportion of assortative mating was >95%—even in the absence of temporal or spatial isolation.
Do 15-Month-Old Infants Understand False Beliefs?
Authors: Onishi Kristine H. , Baillargeon Renée
Published: April 2005

For more than two decades, researchers have argued that young children do not understand mental states such as beliefs. Part of the evidence for this claim comes from preschoolers' failure at verbal tasks that require the understanding that others may hold false beliefs. Here, we used a novel nonverbal task to examine 15-month-old infants' ability to predict an actor's behavior on the basis of her true or false belief about a toy's hiding place. Results were positive, supporting the view that, from a young age, children appeal to mental states—goals, perceptions, and beliefs—to explain the behavior of others.
High-Resolution NMR Spectroscopy with a Portable Single-Sided Sensor
Authors: Perlo Juan , Demas Vasiliki , Casanova Federico , Meriles Carlos A. , Reimer Jeffrey , Pines Alexander , Blümich Bernhard
Published: April 2005

We report construction of a portable nuclear magnetic resonance sensor with a single-sided open probe design. The resulting magnetic field inhomogeneity is compensated by a pulse sequence that takes advantage of parallel inhomogeneity in the applied radio frequency field. We can thereby acquire fluorine-19 spectra of liquid fluorocarbons with 8 parts per million resolution, surmounting the long-standing obstacle of obtaining chemical shift information with open probe instruments.
The Structure of a Retinal-Forming Carotenoid Oxygenase
Authors: Kloer Daniel P. , Ruch Sandra , Al-Babili Salim , Beyer Peter , Schulz Georg E.
Published: April 2005

Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe
2+
-4-His arrangement at the axis of a seven-bladed β-propeller chain fold covered by a dome formed by six large loops. The Fe
2+
is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe
2+
and cleaved by oxygen.
Functional Genomic Analysis of the Wnt-Wingless Signaling Pathway
Authors: DasGupta Ramanuj , Kaykas Ajamete , Moon Randall T. , Perrimon Norbert
Published: April 2005

The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in
Drosophila
cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which ∼18% are associated with human disease. Functional assays of selected genes from the cell-based screen in
Drosophila
, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.
Formation of a Carbon-Carbon Triple Bond by Coupling Reactions In Aqueous Solution
Authors: Bino Avi , Ardon Michael , Shirman Elijah
Published: April 2005

Formation of a carbon-carbon triple bond by coupling reactions usually takes place at high temperatures, in anhydrous media and anaerobic conditions. We describe the formation of a carbon-carbon triple bond at room temperature in an aqueous solution exposed to the atmosphere. Two ethylidyne ligands of a trimolybdenum cluster coupled spontaneously to form 2-butyne. This unexpected result demonstrates the plausibility of alkylidyne chain lengthening and metathesis processes under ambient, environmentally friendly conditions.
Big Book on Our Gas Giant
Authors: Rowan Linda
Published: April 2005

Jupiter
The Planet, Satellites and Magnetosphere.
Fran Bagenal, Timothy E. Dowling, and William B. McKinnon, Eds.
. Cambridge University Press, Cambridge, 2004. 731 pp. + CD-ROM. $150, £85. ISBN 0-521-81808-7. Cambridge Planetary Science.

Synthesizing findings from 6 spacecraft fly-bys and the Galileo mission, the contributors provide a comprehensive account of our current understanding of the jovian system.
The Blind Godmaker
Authors: Shermer Michael
Published: April 2005

Dawkins' God
Genes, Memes, and the Meaning of Life.
By Alister McGrath
. Blackwell, Oxford, 2004. 208 pp. $54.95, £45. ISBN 1-4051-2539-X. Paper, $18.95, £9.99. ISBN 1-4051-2538-1.

The author, a one-time militant atheist who converted to Christianity, offers an analysis of Dawkins's writings that pays particular attention to his comments on religion.
Surface Hydrophobicity Changes of Two
Candida albicans
Serotype B
mnn4
Δ Mutants
Authors: Singleton David R. , Masuoka James , Hazen Kevin C.
Published: April 2005

Cell surface hydrophobicity (CSH) of
Candida
species enhances virulence by promoting adhesion to host tissues. Biochemical analysis of yeast cell walls has demonstrated that the most significant differences between hydrophobic and hydrophilic yeasts are found in the acid-labile fraction of
Candida albicans
phosphomannoprotein, suggesting that this fraction is important in the regulation of the CSH phenotype. The acid-labile fraction of
C. albicans
is unique among fungi, in that it is composed of an extended polymer of β-1,2-mannose linked to the acid-stable region of the
N
-glycan by a phosphodiester bond.
C. albicans
serotype A and B strains both contain a β-1,2-mannose acid-labile moiety, but only serotype A strains contain additional β-1,2-mannose in the acid-stable region. A knockout of the
C. albicans
homolog of the
Saccharomyces cerevisiae MNN4
gene was generated in two serotype B
C. albicans
patient isolates by using homologous gene replacement techniques, with the anticipation that they would be deficient in the acid-labile fraction and, therefore, demonstrate perturbed CSH. The resulting
mnn4
Δ-deficient derivative has no detectable phosphate-linked β-1,2-mannose in its cell wall, and hydrophobicity is increased significantly under conditions that promote the hydrophilic phenotype. The
mnn4
Δ mutant also demonstrates an unanticipated perturbation in the acid-stable mannan fraction. The present study reports the first genetic knockout constructed in a serotype B
C. albicans
strain and represents an important step for dissecting the regulation of CSH.
Combinatorial Repression of the Hypoxic Genes of
Saccharomyces cerevisiae
by DNA Binding Proteins Rox1 and Mot3
Authors: Klinkenberg Lee G. , Mennella Thomas A. , Luetkenhaus Katharina , Zitomer Richard S.
Published: April 2005

The hypoxic genes of
Saccharomyces cerevisiae
are transcriptionally repressed during aerobic growth through recruitment of the Ssn6/Tup1 general repression complex by the DNA binding protein Rox1. A second DNA binding protein Mot3 enhances repression of some hypoxic genes. Previous studies characterized the role of Mot3 at the hypoxic
ANB1
gene as promoting synergy among one Mot3 site and two Rox1 sites comprising operator A of that gene. Here we studied the role of Mot3 in enhancing repression by Rox1 at another hypoxic gene,
HEM13
, which is less strongly regulated than
ANB1
and has a very different arrangement of Rox1 and Mot3 binding sites. By assessing the effects of deleting Rox1 and Mot3 sites individually and in combination, we found that the major repression of
HEM13
occurred through three Mot3 sites closely spaced with a single Rox1 site. While the Mot3 sites functioned additively, they enhanced repression by the single Rox1 site, and the presence of Rox1 enhanced the additive effects of the Mot3 sites. In addition, using a Rox1-Ssn6 fusion protein, we demonstrated that Mot3 enhances Rox1 repression through helping recruit the Ssn6/Tup1 complex. Chromatin immunoprecipitation assays indicated that Rox1 stabilized Mot3 binding to DNA. Integrating these results, we were able to devise a set of rules that govern the combinatorial interactions between Rox1 and Mot3 to achieve differential repression.
Contribution of CAF-I to Anaphase-Promoting-Complex-Mediated Mitotic Chromatin Assembly in
Saccharomyces cerevisiae
Authors: Harkness Troy A. A. , Arnason Terra G. , Legrand Charmaine , Pisclevich Marnie G. , Davies Gerald F. , Turner Emma L.
Published: April 2005

The anaphase-promoting complex (APC) is required for mitotic progression and genomic stability. Recently, we demonstrated that the APC is also required for mitotic chromatin assembly and longevity. Here, we investigated the role the APC plays in chromatin assembly. We show that
apc5

CA

mutations genetically interact with the CAF-I genes as well as
ASF1
,
HIR1
, and
HIR2
. When present in multiple copies, the individual CAF-I genes,
CAC1
,
CAC2
, and
MSI1
, suppress
apc5

CA

phenotypes in a CAF-1- and Asf1p-independent manner. CAF-I and the APC functionally overlap, as
cac1Δ cac2Δ msi1Δ
(
caf1Δ
) cells expressing
apc5

CA

exhibit a phenotype more severe than that of
apc5

CA

or
caf1Δ
. The Ts
−
phenotypes observed in
apc5

CA

and
apc5

CA

caf
mutants may be rooted in compromised histone metabolism, as coexpression of histones H3 and H4 suppressed the Ts
−
defects. Synthetic genetic interactions were also observed in
apc5

CA

asf1Δ
cells. Furthermore, increased expression of genes encoding Asf1p, Hir1p, and Hir2p suppressed the
apc5

CA

Ts
−
defect in a CAF-I-dependent manner. Together, these results suggest the existence of a complex molecular mechanism controlling APC-dependent chromatin assembly. Our data suggest the APC functions with the individual CAF-I subunits, Asf1p, and the Hir1p and Hir2p proteins. However, Asf1p and an intact CAF-I complex are dispensable for CAF-I subunit suppression, whereas CAF-I is necessary for
ASF1
,
HIR1
, and
HIR2
suppression of
apc5

CA

phenotypes. We discuss the implications of our observations.
Surface Localization of the Yps3p Protein of
Histoplasma capsulatum
Authors: Bohse Megan L. , Woods Jon P.
Published: April 2005

The
YPS3
gene of
Histoplasma capsulatum
encodes a protein that is both resident in the cell wall and also released into the culture medium. This protein is produced only during the pathogenic yeast phase of infection and is also expressed differently in
H. capsulatum
strains that differ in virulence. We investigated the cellular localization of Yps3p. We demonstrated that the cell wall fraction of Yps3p was surface localized in restriction fragment length polymorphism class 2 strains. We also established that Yps3p released into the G217B culture supernatant binds to the surface of strains that do not naturally express the protein. This binding was saturable and occurred within 5 min of exposure and occurred similarly with live and heat-killed
H. capsulatum
. Flow cytometric analysis of
H. capsulatum
after enzymatic treatments was consistent with Yps3p binding to chitin, a carbohydrate polymer that is a component of fungal cell walls. Polysaccharide binding assays demonstrated that chitin but not cellulose binds to and extracts Yps3p from culture supernatants.
PldB, a Putative Phospholipase D Homologue in
Dictyostelium discoideum
Mediates Quorum Sensing during Development
Authors: Chen Yi , Rodrick Vanessa , Yan Yi , Brazill Derrick
Published: April 2005

Quorum sensing, also known as cell-density sensing in the unicellular eukaryote
Dictyostelium discoideum
, is required for efficient entry into the differentiation and development segment of its life cycle. Quorum sensing is accomplished by simultaneously secreting and sensing the glycoprotein Conditioned Medium Factor, or CMF. When the density of starving cells is high, CMF levels are high, which leads to aggregation followed by development. Here, we describe the role of
pldB
, a gene coding for a putative phospholipase D (PLD) homologue, in quorum sensing. We find that in submerged culture, adding butanol, an inhibitor of PLD-catalyzed phosphatidic acid production, allows cells to bypass the requirement for CMF mediated quorum sensing and aggregate at low cell density. Deletion of
pldB
mimics the presence of butanol, allowing cells to aggregate at low cell density.
pldB
−
cells also initiate and finish aggregation rapidly. Analysis of early developmental gene expression in
pldB
−
cells reveals that the cyclic AMP receptor cAR1 is expressed at higher levels earlier than in wild-type cells, which could explain the rapid aggregation phenotype. As would be predicted, cells overexpressing
pldB
are unable to aggregate even at high cell density. Adding CMF to these
pldB
−
overexpressing cells does not rescue aggregation. Both of these phenotypes are cell autonomous, as mixing a small number of
pldB
−
cells with wild-type cells does not cause the wild-type cells to behave like
pldB
−
cells.
Identification and Gene Expression Analysis of a Large Family of Transmembrane Kinases Related to the Gal/GalNAc Lectin inEntamoeba histolytica
Authors: Beck David L. , Boettner Douglas R. , Dragulev Bojan , Ready Kim , Nozaki Tomoyoshi , Petri William A.
Published: April 2005

We identified in theEntamoeba histolyticagenome a family of over 80 putative transmembrane kinases (TMKs). The TMK extracellular domains had significant similarity to the intermediate subunit (Igl) of the parasite Gal/GalNAc lectin. The closest homolog to theE. histolyticaTMK kinase domain was a cytoplasmic dual-specificity kinase, SplA, fromDictyostelium discoideum. Sequence analysis of the TMK family demonstrated similarities to both serine/threonine and tyrosine kinases. TMK genes from each of six phylogenetic groups were expressed as mRNA in trophozoites, as assessed by spotted oligoarray and real-time PCR assays, suggesting nonredundant functions of the TMK groups for sensing and responding to extracellular stimuli. Additionally, we observed changes in the expression profile of the TMKs in continuous culture. Antisera produced against the conserved kinase domain identified proteins of the expected molecular masses of the expressed TMKs. Confocal microscopy with anti-TMK kinase antibodies revealed a focal distribution of the TMKs on the cytoplasmic face of the trophozoite plasma membrane. We conclude thatE. histolyticaexpresses members of each subgroup of TMKs. The presence of multiple receptor kinases in the plasma membrane offers for the first time a potential explanation of the ability of the parasite to respond to the changing environment of the host.
Pairwise Knockdowns of cdc2-Related Kinases (CRKs) in
Trypanosoma brucei
Identified the CRKs for G
1
/S and G
2
/M Transitions and Demonstrated Distinctive Cytokinetic Regulations between Two Developmental Stages of the Organism
Authors: Tu Xiaoming , Wang Ching C.
Published: April 2005

Expression of the cdc2-related kinase 3 (CRK3) together with expression of CRK1, -2, -4, or -6, were knocked down in pairs in the procyclic and bloodstream forms of
Trypanosoma brucei
, using the RNA interference technique. Double knockdowns of CRK3 and CRK2, CRK4, or CRK6 exerted significant growth inhibition and enriched the cells in G
2
/M phase, whereas a CRK3 plus CRK1 (CRK3 + CRK1) knockdown arrested cells in both G
1
/S and G
2
/M transitions. Thus, CRK1 and CRK3 are apparently the kinases regulating the G
1
/S and G
2
/M checkpoint passages, respectively, whereas the other CRKs are probably playing only minor roles in cell cycle regulation. A CRK1 + CRK2 knockdown in the procyclic form was found to cause aberrant posterior cytoskeletal morphogenesis (X. M. Tu and C. C. Wang, Mol. Biol. Cell
16:
97-105, 2005). A CRK3 + CRK2 knockdown, however, did not lead to such a change, suggesting that CRK2 depletion can lead to the abnormal morphogenesis only when procyclic-form cells are arrested in the G
1
phase. The G
2
/M-arrested procyclic form produces up to 20% stumpy anucleated cells (zoids) in the population, suggesting that cytokinesis and cell division are not blocked by mitotic arrest but are apparently driven to completion by the kinetoplast cycle. In the bloodstream form, however, G
2
/M arrest resulted in little zoid formation but, instead, enriched a population of cells each containing multiple kinetoplasts, basal bodies, and flagella and an aggregate of multiple nuclei, indicating failure in entering cytokinesis. The two different cytokinetic regulations between two distinct stage-specific forms of the same organism may provide an interesting and useful model for further understanding the evolution of cytokinetic control among eukaryotes.
Intracellular Role of Adenylyl Cyclase in Regulation of Lateral Pseudopod Formation duringDictyosteliumChemotaxis
Authors: Stepanovic Vesna , Wessels Deborah , Daniels Karla , Loomis William F. , Soll David R.
Published: April 2005

Cyclic AMP (cAMP) functions as the extracellular chemoattractant in the aggregation phase ofDictyosteliumdevelopment. There is some question, however, concerning what role, if any, it plays intracellularly in motility and chemotaxis. To test for such a role, the behavior of null mutants ofacaA, the adenylyl cyclase gene that encodes the enzyme responsible for cAMP synthesis during aggregation, was analyzed in buffer and in response to experimentally generated spatial and temporal gradients of extracellular cAMP.acaA−cells were defective in suppressing lateral pseudopods in response to a spatial gradient of cAMP and to an increasing temporal gradient of cAMP.acaA−cells were incapable of chemotaxis in natural waves of cAMP generated by majority control cells in mixed cultures. These results indicate that intracellular cAMP and, hence, adenylyl cyclase play an intracellular role in the chemotactic response. The behavioral defects ofacaA−cells were surprisingly similar to those of cells of null mutants ofregA, which encodes the intracellular phosphodiesterase that hydrolyzes cAMP and, hence, functions opposite adenylyl cyclase A (ACA). This result is consistent with the hypothesis that ACA and RegA are components of a receptor-regulated intracellular circuit that controls protein kinase A activity. In this model, the suppression of lateral pseudopods in the front of a natural wave depends on a complete circuit. Hence, deletion of any component of the circuit (i.e., RegA or ACA) would result in the same chemotactic defect.
Systematic Deletion Analysis of Fission Yeast Protein Kinases
Authors: Bimbó Andrea , Jia Yonghui , Poh Siew Lay , Karuturi R. Krishna Murthy , den Elzen Nicole , Peng Xu , Zheng Liling , O'Connell Matthew , Liu Edison T. , Balasubramanian Mohan K. , Liu Jianhua
Published: April 2005

Eukaryotic protein kinases are key molecules mediating signal transduction that play a pivotal role in the regulation of various biological processes, including cell cycle progression, cellular morphogenesis, development, and cellular response to environmental changes. A total of 106 eukaryotic protein kinase catalytic-domain-containing proteins have been found in the entire fission yeast genome, 44% (or 64%) of which possess orthologues (or nearest homologues) in humans, based on sequence similarity within catalytic domains. Systematic deletion analysis of all putative protein kinase-encoding genes have revealed that 17 out of 106 were essential for viability, including three previously uncharacterized putative protein kinases. Although the remaining 89 protein kinase mutants were able to form colonies under optimal growth conditions, 46% of the mutants exhibited hypersensitivity to at least 1 of the 17 different stress factors tested. Phenotypic assessment of these mutants allowed us to arrange kinases into functional groups. Based on the results of this assay, we propose also the existence of four major signaling pathways that are involved in the response to 17 stresses tested. Microarray analysis demonstrated a significant correlation between the expression signature and growth phenotype of kinase mutants tested. Our complete microarray data sets are available at
http://giscompute.gis.a-star.edu.sg/∼gisljh/kinome
.
Maternal Inheritance and Stage-Specific Variation of the Apicoplast in
Toxoplasma gondii
during Development in the Intermediate and Definitive Host
Authors: Ferguson David J. P. , Henriquez Fiona L. , Kirisits Michael J. , Muench Stephen P. , Prigge Sean T. , Rice David W. , Roberts Craig W. , McLeod Rima L.
Published: April 2005

The structure and location of
Toxoplasma gondii
apicoplasts were examined in intermediate and definitive hosts and shown to vary in a stage-specific manner. Immunocytochemistry and electron microscopy studies were used to identify changes in the morphology of apicoplasts and in their enoyl reductase (ENR) content during asexual and sexual development. Apicoplasts in tachyzoites were small, multimembraned organelles anterior to nuclei that divided and segregated with the nuclei during endodyogeny. In nonproliferating bradyzoites within mature tissue cysts (1 to 24 months), apicoplasts had high levels of ENR. During coccidian development, asexual multiplication (endopolygeny), resulting in simultaneous formation of up to 30 daughters (merozoites), involved an initial growth phase associated with repeated nuclear divisions during which apicoplasts appeared as single, elongated, branched structures with increased levels of ENR. At initiation of merozoite formation, enlarged apicoplasts divided simultaneously, with constrictions, into portions that segregated to developing daughters. In sexual stages, apicoplast division did not occur during microgametogony, and apicoplasts were absent from the microgametes that were formed. In contrast, during macrogametogony, the apicoplast appeared as a large, branched, perinuclear structure that had very high levels of ENR in the absence of nuclear division. Marked increases in the size of apicoplasts and levels of ENR may be related to requirements of the macrogametocytes to synthesize and store all components necessary for oocyst formation and subsequent extracellular sporulation. Thus, it is shown that apicoplasts are present and contain ENR in all
T. gondii
life cycle stages except microgametes, which will result in maternal inheritance of the organelle.
Proteomic Analysis of Phagocytosis in the Enteric Protozoan Parasite
Entamoeba histolytica
Authors: Okada Mami , Huston Christopher D. , Mann Barbara J. , Petri William A. , Kita Kiyoshi , Nozaki Tomoyoshi
Published: April 2005

Proteomic analysis of phagosomes isolated from
Entamoeba histolytica
by liquid chromatography and mass spectrometry identified 85 proteins involved in surface recognition, actin cytoskeleton rearrangement, vesicular trafficking, and degradation. Phagosome localization of representative proteins was verified by immunofluorescence assay. This study should provide a basis for molecular identification and characterization of phagosome biogenesis.