bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the CyanobacteriumSynechocystissp. Strain PCC 6803
Authors: Eisenhut Marion , Huege Jan , Schwarz Doreen , Bauwe Hermann , Kopka Joachim , Hagemann Martin
Published: October 2008

The amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2-phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO2 conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading.
A Novel 2-Oxoacid-Dependent Dioxygenase Involved in the Formation of the Goiterogenic 2-Hydroxybut-3-enyl Glucosinolate and Generalist Insect Resistance in Arabidopsis
Authors: Hansen Bjarne G. , Kerwin Rachel E. , Ober James A. , Lambrix Virginia M. , Mitchell-Olds Thomas , Gershenzon Jonathan , Halkier Barbara A. , Kliebenstein Daniel J.
Published: October 2008

Glucosinolates are secondary metabolites found almost exclusively in the order Brassicales. They are synthesized from a variety of amino acids and can have numerous side chain modifications that control biological function. We investigated the biosynthesis of 2-hydroxybut-3-enyl glucosinolate, which has biological activities including toxicity to Caenorhabditis elegans, inhibition of seed germination, induction of goiter disease in mammals, and production of bitter flavors in Brassica vegetable crops. Arabidopsis (Arabidopsis thaliana) accessions contain three different patterns of 2-hydroxybut-3-enyl glucosinolate accumulation (present in leaves and seeds, seeds only, or absent) corresponding to three different alleles at a single locus, GSL-OH. Fine-scale mapping of the GSL-OH locus identified a 2-oxoacid-dependent dioxygenase encoded by At2g25450 required for the formation of both 2R- and 2S-2-hydroxybut-3-enyl glucosinolate from the precursor 3-butenyl glucosinolate precursor. Naturally occurring null mutations and T-DNA insertional mutations in At2g25450 exhibit a complete absence of 2-hydroxybut-3-enyl glucosinolate accumulation. Analysis of herbivory by the generalist lepidopteran Trichoplusia ni showed that production of 2-hydroxybut-3-enyl glucosinolate provides increased resistance. These results show that At2g25450 is necessary for the hydroxylation of but-3-enyl glucosinolate to 2-hydroxybut-3-enyl glucosinolate in planta and that this metabolite increases resistance to generalist herbivory.
The Arabidopsis Calcium Sensor Calcineurin B-Like 3 Inhibits the 5′-Methylthioadenosine Nucleosidase in a Calcium-Dependent Manner
Authors: Oh Seung-Ick , Park Jimyeong , Yoon Sunhee , Kim Yungyeong , Park Soojin , Ryu Migyeong , Nam Min Jung , Ok Sung Han , Kim Jeong-Kook , Shin Jeong-Sheop , Kim Kyung-Nam
Published: October 2008

Calcineurin B-like (CBL) proteins represent a unique family of calcium sensors in plant cells. Sensing the calcium signals elicited by a variety of abiotic stresses, CBLs transmit the information to a group of serine/threonine protein kinases (CBL-interacting protein kinases [CIPKs]), which are currently known as the sole targets of the CBL family. Here, we report that the CBL3 member of this family has a novel interaction partner in addition to the CIPK proteins. Extensive yeast two-hybrid screenings with CBL3 as bait identified an interesting Arabidopsis (Arabidopsis thaliana) cDNA clone (named AtMTAN, for 5′-methylthioadenosine nucleosidase), which encodes a polypeptide similar to EcMTAN from Escherichia coli. Deletion analyses showed that CBL3 utilizes the different structural modules to interact with its distinct target proteins, CIPKs and AtMTAN. In vitro and in vivo analyses verified that CBL3 and AtMTAN physically associate only in the presence of Ca2+. In addition, we empirically demonstrated that the AtMTAN protein indeed possesses the MTAN activity, which can be inhibited specifically by Ca2+-bound CBL3. Overall, these findings suggest that the CBL family members can relay the calcium signals in more diverse ways than previously thought. We also discuss a possible mechanism by which the CBL3-mediated calcium signaling regulates the biosynthesis of ethylene and polyamines, which are involved in plant growth and development as well as various stress responses.
Enhanced heat loss responses induced by short‐term endurance training in exercising women
Authors: Ichinose Tomoko K. , Inoue Yoshimitsu , Hirata Mari , Shamsuddin A. K. M. , Kondo Narihiko
Published: October 2008

We investigated the effects of short‐term endurance training and detraining on sweating and cutaneous vasodilatation during exercise in young women, taking into account changes in maximal oxygen uptake (
) and the phase of the menstrual cycle. Eleven untrained women participated in endurance training; cycle exercise at ∼60%
for 60 min day−1, 4–5 days week−1 (30°C, 45% relative humidity) for three complete menstrual cycles. The standard exercise test consisted of exercise at 50%
for 30 min (25°C, 45% relative humidity), and was conducted before training (Pre), during training sessions (T1, T2 and T3) and after cessation of training (D1 and D2). Values of
increased significantly from 32.7 ± 1.2 to 37.8 ± 1.2 ml min−1 kg−1 at the end of the training. Local sweat rate in the chest and thigh, but not in the back and forearm, were significantly greater during T1 and T2 only in women who started training from the midfollicular phase. Cutaneous blood flow did not change with training. The threshold oesophageal temperatures for heat loss responses were significantly decreased during T1 versus Pre (averaged values for each body site: sweating, 37.49 ± 0.08 versus 37.22 ± 0.12°C; and cutaneous vasodilatation, 37.40 ± 0.07 versus 37.17 ± 0.10°C) and maintained through T3; the sensitivities of heat loss responses were not altered. These changes returned to the Pre level by D1. Our data indicate that physical training improves heat loss responses by decreasing the threshold temperatures and that these effects occur within a month of training and disappear within a month after cessation of training. The degree of increase in sweating with training differs among body sites and might be affected by the phase of the menstrual cycle.
Neuromodulators of peripheral cardiac sympatho‐vagal balance
Authors: Herring Neil , Paterson David J.
Published: October 2008

The traditional model of efferent cardiac noradrenaline and acetylcholine release being driven solely via brainstem integration of circulatory reflex afferent input needs to be modified in the light of the discovery of numerous local cardiac factors that impact on peripheral neuronal neurotransmitter release. These neuromodulators can be intrinsic to sympathetic ganglia or vagal neurons (such as neuronal nitric oxide synthase), act as cotransmitters between these neuronal populations (such as neuropeptide Y) or are released from the myocardium itself to act on neurons in a paracrine manner (such as natriuretic peptides). Both myocardial infarction and congestive heart failure are characterized by enhanced regulation of these neuromodulators. This review will focus on recent evidence that nitric oxide, natriuretic peptides and neuropeptide Y act by converging on neuronal cyclic nucleotide‐dependent pathways to alter the autonomic phenotype in both health and disease.
Myocardial overexpression of adenine nucleotide translocase 1 ameliorates diabetic cardiomyopathy in mice
Authors: Wang Yong , Ebermann Linda , Sterner‐Kock Anja , Wika Sylwia , Schultheiss Heinz‐Peter , Dörner Andrea , Walther Thomas
Published: October 2008

Mitochondrial dysfunction is implicated in the pathogenesis of diabetic cardiomyopathy, a common complication of diabetes. Adenosine nucleotide translocase (ANT) translocates ADP/ATP across the inner mitochondrial membrane. Our study aimed to test the hypothesis that overexpression of ANT1 in cardiomyocytes has cardioprotective effects in diabetic cardiomyopathy induced by streptozotocin (STZ). Mice specifically overexpressing murine ANT1 in the heart were generated using α‐myosin heavy chain promoter. Expression of ANT1 mRNA and protein in hearts was characterized by real‐time polymerase chain reaction and Western blot analysis. Five‐ to 6‐month‐old male transgenic mice and their age‐matched wild‐type littermates were subjected to type 1 diabetes induced by STZ. Six weeks later, haemodynamic measurement was performed to assess cardiac function. Ventricular mRNA expression of atrial natriuretic peptide, a molecular marker of heart failure, was characterized by RNase‐protection assay. Both ANT1 mRNA and ANT1 protein were specifically overexpressed in the heart of transgenic mice. Heart weight was decreased and cardiac function was dramatically impaired in wild‐type mice 6 weeks after induction of diabetes, but ANT1 overexpression prevented these significant changes. The mRNA expression level of atrial natriuretic peptide confirmed the haemodynamic findings, being upregulated in wild‐type mice receiving STZ, but showing no statistical differences in ANT1 transgenic mice. Cardiomyocyte‐restricted overexpression of ANT1 prevents the development of diabetic cardiomyopathy; therefore, accelerated ADP/ATP exchange could be a new promising target to treat diabetic cardiomyopathy.
Receptor-Like Kinase ACR4 Restricts Formative Cell Divisions in the
Arabidopsis
Root
Authors: De Smet Ive , Vassileva Valya , De Rybel Bert , Levesque Mitchell P. , Grunewald Wim , Van Damme Daniël , Van Noorden Giel , Naudts Mirande , Van Isterdael Gert , De Clercq Rebecca , Wang Jean Y. , Meuli Nicholas , Vanneste Steffen , Friml Jiří , Hilson Pierre , Jürgens Gerd , Ingram Gwyneth C. , Inzé Dirk , Benfey Philip N. , Beeckman Tom
Published: October 2008

During the development of multicellular organisms, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of
Arabidopsis
as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.
Functional Traits and Niche-Based Tree Community Assembly in an Amazonian Forest
Authors: Kraft Nathan J. B. , Valencia Renato , Ackerly David D.
Published: October 2008

It is debated whether species-level differences in ecological strategy, which play a key role in much of coexistence theory, are important in structuring highly diverse communities. We examined the co-occurrence patterns of over 1100 tree species in a 25-hectare Amazonian forest plot in relation to field-measured functional traits. Using a null model approach, we show that co-occurring trees are often less ecologically similar than a niche-free (neutral) model predicts. Furthermore, we find evidence for processes that simultaneously drive convergence and divergence in key aspects of plant strategy, suggesting that at least two distinct niche-based processes are occurring. Our results show that strategy differentiation among species contributes to the maintenance of diversity in one of the most diverse tropical forests in the world.
Detection of First-Order Liquid/Liquid Phase Transitions in Yttrium Oxide-Aluminum Oxide Melts
Authors: Greaves G. N. , Wilding M. C. , Fearn S. , Langstaff D. , Kargl F. , Cox S. , Van Q. Vu , Majérus O. , Benmore C. J. , Weber R. , Martin C. M. , Hennet L.
Published: October 2008

We combine small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) with aerodynamic levitation techniques to study in situ phase transitions in the liquid state under contactless conditions. At very high temperatures, yttria-alumina melts show a first-order transition, previously inferred from phase separation in quenched glasses. We show how the transition coincides with a narrow and reversible maximum in SAXS indicative of liquid unmixing on the nanoscale, combined with an abrupt realignment in WAXS features related to reversible shifts in polyhedral packing on the atomic scale. We also observed a rotary action in the suspended supercooled drop driven by repetitive transitions (a polyamorphic rotor) from which the reversible changes in molar volume (1.2 ± 0.2 cubic centimeters) and entropy (19 ± 4 joules mole–1kelvin–1) can be estimated.
Midbody Targeting of the ESCRT Machinery by a Noncanonical Coiled Coil in CEP55
Authors: Lee Hyung Ho , Elia Natalie , Ghirlando Rodolfo , Lippincott-Schwartz Jennifer , Hurley James H.
Published: October 2008

The ESCRT (endosomal sorting complex required for transport) machinery is required for the scission of membrane necks in processes including the budding of HIV-1 and cytokinesis. An essential step in cytokinesis is recruitment of the ESCRT-I complex and the ESCRT-associated protein ALIX to the midbody (the structure that tethers two daughter cells) by the protein CEP55. Biochemical experiments show that peptides from ALIX and the ESCRT-I subunit TSG101 compete for binding to the ESCRT and ALIX-binding region (EABR) of CEP55. We solved the crystal structure of EABR bound to an ALIX peptide at a resolution of 2.0 angstroms. The structure shows that EABR forms an aberrant dimeric parallel coiled coil. Bulky and charged residues at the interface of the two central heptad repeats create asymmetry and a single binding site for an ALIX or TSG101 peptide. Both ALIX and ESCRT-I are required for cytokinesis, which suggests that multiple CEP55 dimers are required for function.
Experiencing Physical Warmth Promotes Interpersonal Warmth
Authors: Williams Lawrence E. , Bargh John A.
Published: October 2008

“Warmth” is the most powerful personality trait in social judgment, and attachment theorists have stressed the importance of warm physical contact with caregivers during infancy for healthy relationships in adulthood. Intriguingly, recent research in humans points to the involvement of the insula in the processing of both physical temperature and interpersonal warmth (trust) information. Accordingly, we hypothesized that experiences of physical warmth (or coldness) would increase feelings of interpersonal warmth (or coldness), without the person's awareness of this influence. In study 1, participants who briefly held a cup of hot (versus iced) coffee judged a target person as having a “warmer” personality (generous, caring); in study 2, participants holding a hot (versus cold) therapeutic pad were more likely to choose a gift for a friend instead of for themselves.
Genetic Compatibility Affects Queen and Worker Caste Determination
Authors: Schwander Tanja , Keller Laurent
Published: October 2008

The development of queen and worker phenotypes in ants has been believed to be largely determined from environmental effects. We provide evidence that the production of discrete phenotypes is also influenced by genetic interaction effects. During the development of eggs into adults, some patrilines among offspring of multiply mated
Pogonomyrmex rugosus
ant queens became more common in workers while others became overrepresented in queens. Controlled crosses showed that these changes stem from some parental genome combinations being compatible for producing one phenotype but less compatible for the other. Genetic interaction effects on caste may be maintained over evolutionary time because the fitness of an allele depends on its genetic background.
H
2
S as a Physiologic Vasorelaxant: Hypertension in Mice with Deletion of Cystathionine γ-Lyase
Authors: Yang Guangdong , Wu Lingyun , Jiang Bo , Yang Wei , Qi Jiansong , Cao Kun , Meng Qinghe , Mustafa Asif K. , Mu Weitong , Zhang Shengming , Snyder Solomon H. , Wang Rui
Published: October 2008

Studies of nitric oxide over the past two decades have highlighted the fundamental importance of gaseous signaling molecules in biology and medicine. The physiological role of other gases such as carbon monoxide and hydrogen sulfide (H
2
S) is now receiving increasing attention. Here we show that H
2
S is physiologically generated by cystathionine γ-lyase (CSE) and that genetic deletion of this enzyme in mice markedly reduces H
2
S levels in the serum, heart, aorta, and other tissues. Mutant mice lacking CSE display pronounced hypertension and diminished endothelium-dependent vasorelaxation. CSE is physiologically activated by calcium-calmodulin, which is a mechanism for H
2
S formation in response to vascular activation. These findings provide direct evidence that H
2
S is a physiologic vasodilator and regulator of blood pressure.
Functional Targeting of DNA Damage to a Nuclear Pore-Associated SUMO-Dependent Ubiquitin Ligase
Authors: Nagai Shigeki , Dubrana Karine , Tsai-Pflugfelder Monika , Davidson Marta B. , Roberts Tania M. , Brown Grant W. , Varela Elisa , Hediger Florence , Gasser Susan M. , Krogan Nevan J.
Published: October 2008

Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how nuclear organization contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors in yeast indicated a functional relationship between a nuclear pore subcomplex and Slx5/Slx8, a small ubiquitin-like modifier (SUMO)–dependent ubiquitin ligase, which we show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering donor sites at the nuclear periphery. This suggests that strand breaks are shunted to nuclear pores for a repair pathway controlled by a conserved SUMO-dependent E3 ligase.
CoRoT Measures Solar-Like Oscillations and Granulation in Stars Hotter Than the Sun
Authors: Michel Eric , Baglin Annie , Auvergne Michel , Catala Claude , Samadi Reza , Baudin Frédéric , Appourchaux Thierry , Barban Caroline , Weiss Werner W. , Berthomieu Gabrielle , Boumier Patrick , Dupret Marc-Antoine , Garcia Rafael A. , Fridlund Malcolm , Garrido Rafael , Goupil Marie-Jo , Kjeldsen Hans , Lebreton Yveline , Mosser Benoît , Grotsch-Noels Arlette , Janot-Pacheco Eduardo , Provost Janine , Roxburgh Ian W. , Thoul Anne , Toutain Thierry , Tiphène Didier , Turck-Chieze Sylvaine , Vauclair Sylvie D. , Vauclair Gérard P. , Aerts Conny , Alecian Georges , Ballot Jérôme , Charpinet Stéphane , Hubert Anne-Marie , Lignières François , Mathias Philippe , Monteiro Mario J. P. F. G. , Neiner Coralie , Poretti Ennio , de Medeiros José Renan , Ribas Ignasi , Rieutord Michel L. , Cortés Teodoro Roca , Zwintz Konstanze
Published: October 2008

Oscillations of the Sun have been used to understand its interior structure. The extension of similar studies to more distant stars has raised many difficulties despite the strong efforts of the international community over the past decades. The CoRoT (Convection Rotation and Planetary Transits) satellite, launched in December 2006, has now measured oscillations and the stellar granulation signature in three main sequence stars that are noticeably hotter than the sun. The oscillation amplitudes are about 1.5 times as large as those in the Sun; the stellar granulation is up to three times as high. The stellar amplitudes are about 25% below the theoretic values, providing a measurement of the nonadiabaticity of the process ruling the oscillations in the outer layers of the stars.
The Extent of Non–Born-Oppenheimer Coupling in the Reaction of Cl(
2
P
) with
para-
H
2
Authors: Wang Xingan , Dong Wenrui , Xiao Chunlei , Che Li , Ren Zefeng , Dai Dongxu , Wang Xiuyan , Casavecchia Piergiorgio , Yang Xueming , Jiang Bin , Xie Daiqian , Sun Zhigang , Lee Soo-Y. , Zhang Dong H. , Werner Hans-Joachim , Alexander Millard H.
Published: October 2008

Elementary triatomic reactions offer a compelling test of our understanding of the extent of electron-nuclear coupling in chemical reactions, which is neglected in the widely applied Born-Oppenheimer (BO) approximation. The BO approximation predicts that in reactions between chlorine (Cl) atoms and molecular hydrogen, the excited spin-orbit state (Cl*) should not participate to a notable extent. We report molecular beam experiments, based on hydrogen-atom Rydberg tagging detection, that reveal only a minor role of Cl*. These results are in excellent agreement with fully quantum-reactive scattering calculations based on two sets of ab initio potential energy surfaces. This study resolves a previous disagreement between theory and experiment and confirms our ability to simulate accurately chemical reactions on multiple potential energy surfaces.
The Structure of a Transcribing T7 RNA Polymerase in Transition from Initiation to Elongation
Authors: Durniak Kimberly J. , Bailey Scott , Steitz Thomas A.
Published: October 2008

Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by ∼45° upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.
Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast
Authors: Bayne Elizabeth H. , Portoso Manuela , Kagansky Alexander , Kos-Braun Isabelle C. , Urano Takeshi , Ekwall Karl , Alves Flavia , Rappsilber Juri , Allshire Robin C.
Published: October 2008

Heterochromatin formation at fission yeast centromeres is directed by RNA interference (RNAi). Noncoding transcripts derived from centromeric repeats are processed into small interfering RNAs (siRNAs) that direct the RNA-induced transcriptional silencing (RITS) effector complex to engage centromere transcripts, resulting in recruitment of the histone H3 lysine 9 methyltransferase Clr4, and hence silencing. We have found that defects in specific splicing factors, but not splicing itself, affect the generation of centromeric siRNAs and consequently centromeric heterochromatin integrity. Moreover, splicing factors physically associate with Cid12, a component of the RNAi machinery, and with centromeric chromatin, consistent with a direct role in RNAi. We propose that spliceosomal complexes provide a platform for siRNA generation and hence facilitate effective centromere repeat silencing.
To Incubate Progress
Authors: Grodal Stine
Published: October 2008

Innovation Nation
. How America Is Losing Its Innovation Edge, Why It Matters, and What We Can Do to Get It Back.
By John Kao
. Free Press, New York, 2007. 319 pp. $26, C$29.99. ISBN 9781416532682.

Kao discusses existing roadblocks to technological innovation (especially in the United States) and suggests actions that he argues will promote the discovery and development of new ideas and thus improve prosperity and economic security.
Direct Imaging of Reconstructed Atoms on TiO
2
(110) Surfaces
Authors: Shibata N. , Goto A. , Choi S.-Y. , Mizoguchi T. , Findlay S. D. , Yamamoto T. , Ikuhara Y.
Published: October 2008

Determining the atomic structures of oxide surfaces is critical for understanding their physical and chemical properties but also challenging because the breaking of atomic bonds in the formation of the surface termination can involve complex reconstructions. We used advanced transmission electron microscopy to directly observe the atomic structure of reduced titania (TiO
2
) (110) surfaces from directions parallel to the surface. In our direct atomic-resolution images, reconstructed titanium atoms at the top surface layer are clearly imaged and are found to occupy the interstitial sites of the TiO
2
structure. Combining observations from two orthogonal directions, the three-dimensional positioning of the Ti interstitials is identified at atomic dimensions and allows a resolution of two previous models that differ in their oxygen stoichiometries.
Gigantic Losses
Authors: Portman Michelle E.
Published: October 2008

Harpoon
Into the Heart of Whaling.
By Andrew Darby
. Da Capo (Perseus), Cambridge, MA, 2008. 320 pp. $25, C$26.95, £14.99. ISBN 9780306816291. Paper, Allen and Unwin, Sydney, Australia, 2007. A$29.95. ISBN 9781741146110.

Darby's account of commercial whaling and efforts to save decimated cetacean populations highlights anti-whaling activists and controversies swirling around the International Whaling Commission.
Flunking Spore
Authors: Bohannon John
Published: October 2008

The blockbuster video game Spore is being marketed as a science-based adventure that brings evolution, cell biology, and even astrophysics to the masses. But after grading the game's science with a team of researchers, the Gonzo Scientist has some bad news.
Development of a Nucleocapsid-Based Human Coronavirus Immunoassay and Estimates of Individuals Exposed to Coronavirus in a U.S. Metropolitan Population
Authors: Severance Emily G. , Bossis Ioannis , Dickerson Faith B. , Stallings Cassie R. , Origoni Andrea E. , Sullens Anne , Yolken Robert H. , Viscidi Raphael P.
Published: October 2008

Coronaviruses cause respiratory infections ranging from common colds to severe acute respiratory syndrome (SARS) in humans. Estimates for exposure to non-SARS coronaviruses are high, particularly for 229E and OC43; however, less information regarding seroprevalence is available for HKU1 and NL63. To measure exposure rates to these four coronavirus strains (229E, HKU1, NL63, and OC43), we devised an immunoassay based on amino- and carboxy-terminally tagged recombinant coronavirus nucleocapsid antigens. Four human and one feline coronavirus antigen were cloned into baculoviruses expressed in insect cells and recovered proteins bound in the solid phase of an enzyme-linked immunosorbent assay-based system. We screened sera from 10 children and 196 adults and established primary cutoff points based on immunoglobulin G (IgG) antibody levels of the predominantly seronegative children. The proportion of seropositive adults for each coronavirus was as follows: 229E, 91.3%; HKU1, 59.2%; NL63, 91.8%; and OC43, 90.8%. No evidence of a significant serological response to the feline coronavirus was observed. Significant associations of coronavirus seropositivity and antibody levels with age, gender, race, socioeconomic status, smoking status, and season of the blood draw were tested with chi-square and regression analyses. The group II coronaviruses (OC43 and HKU1) were significantly associated with race (P≤ 0.009 andP≤ 0.03, respectively). Elevated OC43 IgG levels were further significantly associated with smoking status (P≤ 0.03), as were high NL63 titers with socioeconomic status (P≤ 0.04). The high-level immunoreactivity of each coronavirus was significantly associated with the summer season (P≤ 0.01 to 0.0001). In summary, high rates of exposure to 229E, NL63, and OC43 and a moderate rate of exposure to HKU1 characterized the seroprevalence among individuals in this population. Demographic factors, such as race, smoking status, and socioeconomic status, may confer an increased risk of susceptibility to these viruses.
Serological Diagnosis of Leprosy in Patients in Vietnam by Enzyme-Linked Immunosorbent Assay with
Mycobacterium leprae
-Derived Major Membrane Protein II
Authors: Kai Masanori , Nguyen Phuc Nhu Ha , Hoang Thi Thuy Huong , Nguyen An Hoang , Fukutomi Yasuo , Maeda Yumi , Miyamoto Yuji , Mukai Tetsu , Fujiwara Tsuyoshi , Nguyen Tan Thanh , Makino Masahiko
Published: October 2008

A serological diagnostic test using phenolic glycolipid-I (PGL-I) developed in the 1980s is commercially available, but the method is still inefficient in detecting all forms of leprosy. Therefore, more-specific and -reliable serological methods have been sought. We have characterized major membrane protein II (MMP-II) as a candidate protein for a new serological antigen. In this study, we evaluated the effectiveness of the enzyme-linked immunosorbent assay (ELISA) using the MMP-II antigen (MMP-II ELISA) for detecting antibodies in leprosy patients and patients' contacts in the mid-region of Vietnam and compared to the results to those for the PGL-I method (PGL-I ELISA). The results showed that 85% of multibacillary patients and 48% of paucibacillary patients were positive by MMP-II ELISA. Comparison between the serological tests showed that positivity rates for leprosy patients were higher with MMP-II ELISA than with PGL-I ELISA. Household contacts (HHCs) showed low positivity rates, but medical staff members showed comparatively high positivity rates, with MMP-II ELISA. Furthermore, monitoring of results for leprosy patients and HHCs showed that MMP-II is a better index marker than PGL-I. Overall, the epidemiological study conducted in Vietnam suggests that serological testing with MMP-II would be beneficial in detecting leprosy.
Downregulation of CD40 Ligand Response in Monocytes from Sepsis Patients
Authors: Sinistro Anna , Almerighi Cristiana , Ciaprini Chiara , Natoli Silvia , Sussarello Emanuele , Di Fino Sara , Calò-Carducci Francesca , Rocchi Giovanni , Bergamini Alberto
Published: October 2008

It has been suggested that a defective adaptive immune response contributes to septic immunosuppression. Here, the response of monocytes to CD40 ligand (CD40L) for patients with sepsis due to infection with gram-negative organisms has been analyzed. Compared to cells from controls, monocytes from septic patients showed significantly reduced production of tumor necrosis factor alpha, interleukin-1β (IL-1β), and IL-12 and were unable to acquire high levels of CD80 and CD86 molecules. These alterations were observed at the onset of sepsis and persisted at day 7. However, the ability of monocytes to respond to CD40L stimulation was partially but significantly restored in cells from patients who recovered from sepsis. In addition, costimulation of autologous CD4+T lymphocytes by CD40L-activated monocytes from septic patients failed to induce cell proliferation and gamma interferon production. Finally, the ability of CD40L to rescue monocytes from apoptosis was severely impaired. We conclude that downregulation of the CD40L response may be an appropriate model for the monocyte alteration observed during septic immunosuppression and may help in the development of novel therapeutic strategies.
Evaluation of the Recombinant VlsE-Based Liaison Chemiluminescence Immunoassay for Detection ofBorrelia burgdorferiand Diagnosis of Lyme Disease
Authors: Ledue Thomas B. , Collins Marilyn F. , Young John , Schriefer Martin E.
Published: October 2008

Recent efforts to improve the serologic diagnosis of Lyme disease have included the use of a synthetic peptide (C6) that reproduces the sequence of invariable region 6 of VlsE, the variable surface antigen ofBorrelia burgdorferi. In the present study, the diagnostic performance of DiaSorin's recombinant VlsE-based chemiluminescence immunoassay in 1,947 human serum samples was evaluated. Sensitivity was determined using two serum panels from the CDC. For panel I, we observed sensitivities of 68.4% and 75.6% for subjects with early, localized (n= 19) or disseminated (n= 41) disease, respectively. For panel II, we observed sensitivities of 61.5% and 100% for subjects with early (n= 26) or late-stage (n= 11) disease, respectively. We observed a specificity of 99.5% for healthy donors (n= 600) living either in regions of the United States where the disease is endemic or in regions where it is not endemic. Overall, specificity among 207 potentially cross-reactive sera from subjects who had other spirochetal infections, nonspirochetal infections including bacterial and viral infections, or autoimmune or neurologic disease; who were positive for rheumatoid factor or anti-mouse antibodies; or who had been previously vaccinated for Lyme disease was 93.7%. In a direct comparison of 1,038 prospectively collected samples for Lyme disease testing we observed a relative sensitivity of 70%, a relative specificity of 99.1%, and an overall agreement of 97.1% between the DiaSorin recombinant VlsE chemiluminescence immunoassay and the Immunetics peptide-based C6 enzyme-linked immunosorbent assay.
Improved Sensitivity of Diagnosis of Tuberculosis in Patients in Korea via a Cocktail Enzyme-Linked Immunosorbent Assay Containing the Abundantly Expressed Antigens of the K Strain ofMycobacterium tuberculosis
Authors: Shin A-Rum , Shin Sung Jae , Lee Kil-Soo , Eom Sun-Ho , Lee Seung-Sub , Lee Byung-Soo , Lee Ji-Sook , Cho Sang Nae , Kim Hwa-Jung
Published: October 2008

Tuberculosis (TB) is the leading cause of death from a single infectious agent in Korea. In this study, we compared the proteins present in culture filtrates fromMycobacterium tuberculosisstrain K, which is the dominant clinical isolate in Korea, with those present in culture filtrates fromM. tuberculosisH37Rv. Several differences in expression were detected between the two strains for those proteins with a molecular mass of <20 kDa. ESAT-6, HSP-X, and CFP-10 were found to be abundantly expressed in the strain K culture filtrates by liquid chromatography-electrospray ionization-time of flight mass spectrometry. The serodiagnostic potentials of recombinant antigens rESAT-6, rHSP-X, and rCFP-10 and two native antigens (Ag85 and PstS1) were evaluated by Western blot analysis and enzyme-linked immunosorbent assay (ELISA) using sera collected from 46 TB patients with active disease and 46 healthy controls. As for our ELISA results, HSP-X was superior to the other antigens in terms of sensitivity when a single antigen was employed. The results of a receiver operator characteristic analysis revealed that a cocktail ELISA using all five antigens was significantly more sensitive (77.8%) than the use of a single antigen and offered equivalent specificity; moreover, it produced the largest area under the curve (0.91 versus 0.55 to 0.87). Therefore, a cocktail ELISA containing abundantly expressed antigens enhances the sensitivity of a single antigen and can be a useful diagnostic tool for the detection of active TB.
Real-Time In Vivo Green Fluorescent Protein Imaging of a Murine Leishmaniasis Model as a New Tool for
Leishmania
Vaccine and Drug Discovery
Authors: Mehta Sanjay R. , Huang Robert , Yang Meng , Zhang Xing-Quan , Kolli Bala , Chang Kwang-Poo , Hoffman Robert M. , Goto Yasuyuki , Badaro Roberto , Schooley Robert T.
Published: October 2008

Leishmania
species are obligate intracellular protozoan parasites that cause a broad spectrum of clinical diseases in mammalian hosts. The most frequently used approach to quantify parasites in murine model systems is based on thickness measurements of the footpad or ear after experimental infection. To overcome the limitations of this method, we used a
Leishmania
mutant episomally transfected with enhanced green fluorescent protein, enabling in vivo real-time whole-body fluorescence imaging, to follow the progression of
Leishmania
infection in parasitized tissues. Fluorescence correlated with the number of
Leishmania
parasites in the tissue and demonstrated the real-time efficacy of a therapeutic vaccine. This approach provides several substantial advantages over currently available animal model systems for the in vivo study of immunopathogenesis, prevention, and therapy of leishmaniasis. These include improvements in sensitivity and the ability to acquire real-time data on progression and spread of the infection.
Evaluation of Antigen-Specific T-Cell Responses with a Miniaturized and Automated Method
Authors: Li Pira Giuseppina , Ivaldi Federico , Dentone Chiara , Righi Elda , Del Bono Valerio , Viscoli Claudio , Koopman Gerrit , Manca Fabrizio
Published: October 2008

The evaluation of antigen-specific T-cell responses is helpful for both research and clinical settings. Several techniques can enumerate antigen-responsive T cells or measure their products, but they require remarkable amounts of peripheral blood mononuclear cells (PBMCs). Since screening numerous antigens or testing samples from pediatric or lymphopenic patients is hampered in clinical practice, we refined a miniaturized, high-throughput assay for T-cell immunity. Antigens and cells in 10-μl volumes were dispensed into 1,536-well culture plates precoated with anti-gamma interferon (anti-IFN-γ) antibodies. After being cultured, the wells were developed by enzyme-linked immunosorbent assay for bound cytokine. Miniaturization and automation allowed quantitation of antigen-specific responses on 104PBMCs. This method was applied for epitope mapping of mycobacterial antigens and was used in the clinic to evaluate T-cell immunity to relevant opportunistic pathogens by using small blood samples. A comparison with conventional methods showed similar sensitivity. Therefore, current flow cytometric methods that provide information on frequency and phenotype of specific T cells can be complemented by this assay that provides extensive information on cytokine concentrations and profiles and requires 20- to 50-fold fewer PBMCs than other analytical methods.
Characterization of Extensively Drug-Resistant
Mycobacterium tuberculosis
Clinical Isolates in China
Authors: Sun Zhaogang , Chao Yanjie , Zhang Xuxia , Zhang Jianyuan , Li Yan , Qiu Yunqing , Liu Yi , Nie Lihui , Guo Aizhen , Li Chuanyou
Published: October 2008

Thirteen extensively drug-resistant tuberculosis isolates which were highly resistant to a broad spectrum of antituberculosis drugs were identified from 1,926 clinical isolates in China. They had highly diverse mycobacterial interspersed repetitive-unit-variable-number tandem-repeat patterns. Most, but not all, of the drug target genes had mutations contributing to resistance to the corresponding drug.
Molecular Epidemiology and Phylogenetic Distribution of the
Escherichia coli pks
Genomic Island
Authors: Johnson James R. , Johnston Brian , Kuskowski Michael A. , Nougayrede Jean-Philippe , Oswald Eric
Published: October 2008

Epidemiological and phylogenetic associations of the
pks
genomic island of extraintestinal pathogenic
Escherichia coli
(ExPEC), which encodes the genotoxin colibactin, are incompletely defined.
clbB
and
clbN
(as markers for the 5′ and 3′ regions of the
pks
island, respectively),
clbA
and
clbQ
(as supplemental
pks
island markers), and 12 other putative ExPEC virulence genes were newly sought by PCR among 131 published
E. coli
isolates from hospitalized veterans (62 blood isolates and 69 fecal isolates). Blood and fecal isolates and
clbB
-positive and -negative isolates were compared for 66 newly and previously assessed traits. Among the 14 newly sought traits,
clbB
and
clbN
(colibactin polyketide synthesis system),
hra
(heat-resistant agglutinin), and
vat
(vacuolating toxin) were significantly associated with bacteremia.
clbB
and
clbN
identified a subset within phylogenetic group B2 with extremely high virulence scores and a high proportion of blood isolates. However, by multivariable analysis, other traits were more predictive of blood source than
clbB
and
clbN
were; indeed, among the newly sought traits, only
pic
significantly predicted bacteremia (negative association). By correspondence analysis,
clbB
and
clbN
were closely associated with group B2 and multiple B2-associated traits; by principal coordinate analysis,
clbB
and
clbN
partitioned the data set better than did blood versus fecal source. Thus, the
pks
island was significantly associated with bacteremia, multiple ExPEC-associated virulence genes, and group B2, and within group B2, it identified an especially high-virulence subset. This extends previous work regarding the
pks
island and supports investigation of the colibactin system as a potential therapeutic target.
Multiple-Host Sharing, Long-Term Persistence, and Virulence of
Escherichia coli
Clones from Human and Animal Household Members
Authors: Johnson James R. , Clabots Connie , Kuskowski Michael A.
Published: October 2008

During a 3-year surveillance, six household members (five humans and the family dog) yielded 14
Escherichia coli
clones. Virulence genes, group B2, and having caused cystitis (in the mother or dog) corresponded to colonization endpoints (number of samples, colonies, hosts, and dates). The dog's cystitis clone was the most extensively recovered clone.
Development and Evaluation of a Molecular Assay for Detection of Nontuberculous Mycobacteria by Use of the Cobas Amplicor Platform
Authors: Peter-Getzlaff S. , Lüthy J. , Böddinghaus B. , Böttger E. C. , Springer B.
Published: October 2008

We have developed and evaluated a semiautomated assay for detection of nontuberculous mycobacteria (NTM) from clinical samples based on the Cobas Amplicor
Mycobacterium tuberculosis
test (Roche Diagnostics, Switzerland). A capture probe, specific for mycobacteria at the genus level, was linked to magnetic beads and used for the detection of amplification products obtained by the Cobas Amplicor
M. tuberculosis
assay. We demonstrate that the analytical sensitivity of the genus assay is similar to that of Cobas Amplicor
M. tuberculosis
detection. Four hundred sixteen clinical specimens were evaluated for the presence of NTM DNA. Sensitivities for smear-positive and smear-negative specimens were found to be 100% and 47.9%, respectively. Specificity was 97.7%, the positive predictive value 84.6%, and the negative predictive value 93.1%. The genus assay is easy to perform, produces reliable results, and was found to be a valuable diagnostic tool for rapid diagnosis of infections with NTM. The genus assay has the potential to detect NTM not routinely recovered by culture and to discover new mycobacterial species.
Comparative Study for Determination of
Mycobacterium tuberculosis
Susceptibility to First- and Second-Line Antituberculosis Drugs by the Etest Using 7H11, Blood, and Chocolate Agar
Authors: Coban Ahmet Yilmaz , Bilgin Kemal , Uzun Meltem , Akgunes Alper , Yusof Anne , Durupinar Belma
Published: October 2008

We investigated the performance of blood and chocolate agar as alternatives to Middlebrook 7H11 agar for testing the susceptibility of
Mycobacterium tuberculosis
to first-and second-line drugs by the Etest method. A total of 39 strains of
M. tuberculosis
including 22 multidrug-resistant
M. tuberculosis
strains and 17 susceptible strains were tested. In conclusion, our results showed that chocolate agar gave insufficient growth, needing up to 21 days of incubation, while results on blood agar were comparable to those on Middlebrook 7H11 agar and can be further explored as an alternative for Etest-based susceptibility testing of
M. tuberculosis
.
Rapid Detection of
Mycobacterium tuberculosis
Resistance to Second-Line Drugs by Use of the Manual Mycobacterium Growth Indicator Tube System
Authors: Martin Anandi , von Groll Andrea , Fissette Krista , Palomino Juan Carlos , Varaine Francis , Portaels Françoise
Published: October 2008

The objective of this study was to evaluate the manual mycobacterium growth indicator tube (MGIT) system for the testing of
Mycobacterium tuberculosis
susceptibility to second-line drugs compared to the proportion method. One hundred eighty-eight
M. tuberculosis
isolates were tested for susceptibility to ofloxacin, kanamycin, ethionamide, and capreomycin by the manual MGIT, and results were compared to those obtained with the proportion method on 7H11 agar, considered a reference method. Results for ofloxacin and capreomycin were excellent, with 100% accuracy, and a result of 99.4% accuracy was achieved for kanamycin. For ethionamide, accuracy was lower, with a result of 86.7% compared to that of the proportion method. We proposed the following critical concentrations for the drugs: for ofloxacin, 2.0 μg/ml; for kanamycin, 2.5 μg/ml; for ethionamide, 5 μg/ml; and for capreomycin, 2.5 μg/ml. The time required to obtain results was an average of 8 days by the manual MGIT and 3 weeks by the reference method. Our results show that the manual MGIT is an accurate method for the rapid susceptibility testing of
M. tuberculosis
to second-line drugs. There is no need for a machine when using the manual MGIT, and results can be read with a simple UV lamp or with a semiquantitative reader, which considerably reduces the cost of the method.
Genotypic Antiretroviral Resistance Testing for Human Immunodeficiency Virus Type 1 Integrase Inhibitors by Use of the TruGene Sequencing System
Authors: Paar Christian , Palmetshofer Christina , Flieger Karin , Geit Maria , Kaiser Rolf , Stekel Herbert , Berg Jörg
Published: October 2008

A sequencing assay for detection of mutations conferring resistance to human immunodeficiency virus type 1 (HIV-1) integrase inhibitors raltegravir and elvitegravir was developed using the automated TruGene sequencing system. The assay returned clear sequencing results for samples with ≥500 RNA copies/ml for mutation detection and HIV-1 subtyping across a spectrum of HIV-1 subtypes.