bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Trimeric Peptides That Bind Porcine Parvovirus from Mixtures Containing Human Blood Plasma
Authors: Heldt Caryn L. , Gurgel Patrick V. , Jaykus Lee‐Ann , Carbonell Ruben G.
Published: May 2008

Virus contamination in human therapeutics is of growing concern as more therapeutic products from animal or human sources come into the market. All biopharmaceutical processes are required to have at least two distinct viral clearance steps to remove viruses. Most of these steps work well for enveloped viruses and large viruses, whether enveloped or not. That leaves a class of small non‐enveloped viruses, like parvoviruses and hepatitis A, which are not easily removed by these typical steps. In this study, we report the identification of trimeric peptides that bind specifically to porcine parvovirus (PPV) and their potential use to remove this virus from process solutions. All of the trimeric peptides isolated completely removed all detectable PPV from buffer in the first nine column volumes, corresponding to a clearance of 4.5–5.5 log of infectious virus. When the virus was spiked into a more complex matrix consisting of 7.5% human blood plasma, one of the trimers, WRW, was able to remove all detectable PPV in the first three column volumes, after which human blood plasma began to interfere with the binding of the virus to the peptide resin. These trimer resins removed considerably more virus than weak ion exchange resins. The results of this work indicate that small peptide ligand resins have the potential to be used in virus removal processes where removal of contaminating virus is necessary to ensure product safety.
Microbial Oxidation of Naphthalene to cis‐1,2‐Naphthalene Dihydrodiol Using Naphthalene Dioxygenase in Biphasic Media
Authors: McIver Angela M. , Garikipati SVB Janardhan , Bankole Kehinde S. , Gyamerah Michael , Peeples Tonya L.
Published: May 2008

The selective oxidation of aryl substrates to chiral cis‐1,2‐dihydrodiols is an industrially important reaction for the production of intermediates that can be used to produce fine chemicals, pharmaceuticals, and many other bioactive natural products. More specifically, the oxidation of naphthalene to produce optically pure (+)‐ cis‐(1 R,2 S)‐1,2‐napthalene dihydrodiol (NDHD) to be used as a chiral synthon for specialty chemicals has gained much interest. Escherichia coli JM109(DE3) pDTG141 expresses naphthalene dioxygenase which catalyzes this reaction. Poor substrate solubility and substrate toxicity are barriers to using the power of these enzymes in large‐scale aqueous whole cell systems. A biphasic reaction system was chosen to overcome these barriers. The optimal biphasic conditions for E. coli JM109(DE3) pDTG141 were determined to be 20% dodecane as the organic solvent containing 40 g/L naphthalene. The productivity of the biotransformation using resting cells was 1.75 g‐diol/g‐cdw/h for the first 6 h with 20% organic phase, which was increased from 0.59 g‐diol/g‐cdw/h for growing cells with 40% organic phase. The biocatalytic activity was retained for at least 12 h. The biocatalyst could be recycled for at least four runs in both suspended and immobilized form. The stability of the 12 h recycle was improved by immobilization in calcium alginate beads. The process has been improved both environmentally and economically by reducing the amount of solvent used and by recycling the biocatalyst.
Application of Multivariate Data Analysis for Identification and Successful Resolution of a Root Cause for a Bioprocessing Application
Authors: Kirdar Alime Ozlem , Green Ken D. , Rathore Anurag S.
Published: May 2008

Multivariate Data Analysis (MVDA) can be used for supporting key activities required for successful bioprocessing. These activities include process characterization, process scale‐up, process monitoring, fault diagnosis and root cause analysis. This paper examines an application of MVDA towards root cause analysis for identifying scale‐up differences and parameter interactions that adversely impact cell culture process performance. Multivariate data analysis and modeling were performed using data from small‐scale (2 L), pilot‐scale (2,000 L) and commercial‐scale (15,000 L) batches. The input parameters examined included bioreactor pCO2, glucose, lactate, ammonium, raw materials and seed inocula. The output parameters included product attributes, product titer, viable cell density, cell viability and osmolality. Time course performance variables (daily, initial, peak and end point) were also evaluated. Application of MVDA as a diagnostic tool was successful in identifying the root cause and designing experimental conditions to demonstrate and correct it. Process parameters and their interactions that adversely impact cell culture performance and product attributes were successfully identified. MVDA was successfully used as an effective tool for collating process knowledge and increasing process understanding.
Residue‐Specific Contact Order and Contact Breadth in Single‐Domain Proteins: Implications for Folding as a Function of Chain Elongation
Authors: Kurt Neşe , Mounce Bryan C. , Ellison Paul A. , Cavagnero Silvia
Published: May 2008

Cotranslational protein misfolding and aggregation are often responsible for inclusion body formation during in vivo protein expression. This study addresses the relations between protein folding/misfolding and the distribution of intramolecular interactions across different regions of the polypeptide chain in soluble single‐domain proteins. The sequence regions examined here include the C terminus, which is synthesized last in the cell. Emphasis is placed on two parameters reporting on short‐ and long‐range interactions, i.e., residue‐specific contact order ( RCO) and a new descriptor of intramolecular protein interaction networks denoted as residue‐specific contact breadth ( RCB). RCB illustrates the average spread in sequence of the residues serving as interaction counterparts. We show that both RCO and RCB are maximized at the chain termini for a large fraction of single‐domain soluble proteins. A direct implication of this result is that the C terminus of the polypeptide chain, which is synthesized last during ribosome‐assisted translation, plays a key role in the generation of native‐like structure by establishing long‐range interactions and generating contacts with interaction counterparts widely distributed across the sequence. Comparison of our computational predictions with the experimental behavior of selected proteins shows that the presence and absence of large RCO and RCB at the chain termini correlates with the protein's ability to properly fold either after the C terminus has been synthesized or during chain elongation, respectively.
Transitioning from Fixed-Length Questionnaires to Computer-Adaptive Versions
Authors: Walter Otto B. , Holling Heinz
Published: May 2008

To investigate how an existing questionnaire can be transformed into a computer-adaptive version, we developed an adaptive version of the Interpersonal Competence Questionnaire (ICQ). This adaptive version was based on a representative sample (N = 1934) of respondents who answered 30 items from a German translation of the ICQ. A random half of the sample was used to evaluate test dimensionality, calibrate the items, and model the relation between person parameters and raw total scores. The other random half of the sample was employed to assess the comparability of person parameters and raw scores. After these tests and item calibration, 28 items remained in the item pool. A high correlation was found between raw scores and estimated scores using all items. Raw scores could be predicted accurately from estimated person parameters. These results indicate that our approach is an effective technique for transforming an existing questionnaire into a computer-adaptive version.
Computer Adaptive-Attribute Testing
Authors: Gierl Mark J. , Zhou Jiawen
Published: May 2008

The influence of interdisciplinary forces stemming from developments in cognitive science, mathematical statistics, educational psychology, and computing science are beginning to appear in educational and psychological assessment. Computer adaptive-attribute testing (CA-AT) is one example. The concepts and procedures in CA-AT can be found at the intersection between computer adaptive testing and cognitive diagnostic assessment. CA-AT allows us to fuse the administrative benefits of computer adaptive testing with the psychological benefits of cognitive diagnostic assessment to produce an innovative psychologically-based adaptive testing approach. We describe the concepts behind CA-AT as well as illustrate how it can be used to promote formative, computer-based, classroom assessment.
Some New Developments in Adaptive Testing Technology
Authors: van der Linden Wim J.
Published: May 2008

In an ironic twist of history, modern psychological testing has returned to an adaptive format quite common when testing was not yet standardized. Important stimuli to the renewed interest in adaptive testing have been the development of item-response theory in psychometrics, which models the responses on test items using separate parameters for the items and test takers, and the use of computers in test administration, which enables us to estimate the parameter for a test taker and select the items in real time. This article reviews a selection from the latest developments in the technology of adaptive testing, such as constrained adaptive item selection, adaptive testing using rule-based item generation, multidimensional adaptive testing, adaptive use of test batteries, and the use of response times in adaptive testing.
Validation of a French Adaptation of the Thought Control Ability Questionnaire
Authors: Gay Philippe , d’Acremont Mathieu , Schmidt Ralph E. , Van der Linden Martial
Published: May 2008

Difficulties controlling one’s thoughts have been related to several psychopathological states and are core issues in clinical evaluation and treatment. For this reason, Luciano, Algarabel, Tomás, and Martínez (2005 ) developed the Thought Control Ability Questionnaire (TCAQ). The aim of this study was to propose a reliable, valid French version of this questionnaire. To do so, a two-step methodology was followed. In a first study, the 25 items of the TCAQ were translated into French, and data were collected from a sample of undergraduates. The results revealed that two items were problematic in terms of the questionnaire’s face validity and internal consistency. In a second study, data were collected using the remaining 23 items with a new sample of undergraduates. This time, the results revealed that the 23-item French TCAQ possesses good internal consistency and very high reliability, and fits with a unidimensional model of thought control ability. Convergent validity was found with measures of worry and obsessive symptoms. The usefulness of the TCAQ as a tool for clinicians and researchers in the field of self-regulation is discussed.
Investigating the Structure of Attention
Authors: Krumm Stefan , Schmidt-Atzert Lothar , Eschert Silke
Published: May 2008

The present study examined the influence of different test modi on the relationship between two different sustained attention (SA) tests – one with predominant processing and one with predominant perception demands – and a test of selective attention. Therefore, each attention test was presented in five different modi (paper-pencil, self-paced with item blocks, self-paced with single items, computer-paced with item blocks, computer-paced with single items) and administered to 110 participants. The original versions of different tests correlated only weakly to moderately. But when these tests were modified to correspond in terms of modus, they showed strong correlations. For tests with a predominant perception demand MTMM analyses revealed that the pace modus (self-paced vs. computer-paced) had a higher impact than the tests themselves. A measurement model was established with two attention test factors and three modus factors. The modi of test presentation proved to be distinguishable and accounted for 59.9% of variance in the task set. It is argued that the attention facet tapped by different tests is a function of the task itself, but also of the way this task is presented.
The Assessment of Charismatic Leadership
Authors: Rowold Jens , Kersting Martin
Published: May 2008

This paper examines the psychometric properties of a German version of the Conger-Kanungo Scale (CKS) of charismatic leadership, and compares charismatic leadership with the two leadership paradigms that have dominated theory and practice to date: the transformational/transactional paradigm and the consideration/initiating structure paradigm. An empirical study (N = 404) was conducted to explore aspects of reliability and validity of the CKS. In terms of construct validity, it was demonstrated that the translated instrument had adequate factorial validity. In addition, charismatic leadership measured in terms of the CKS showed convergent validity with respect to both transformational and transactional leadership and initiating structure, and divergent validity with respect to laissez-faire and consideration. In sum, the results contribute to leadership theory (e.g., comparing and contrasting several leadership theories) and practice.
Test of the Construct and Criteria Validity of a German Measure of Organizational Justice
Authors: Streicher Bernhard , Jonas Eva , Maier Günter W. , Frey Dieter , Woschée Ralph , Waßmer Bettina
Published: May 2008

Organizational justice is a well-known and increasingly often measured construct in work-related psychological research, for which, however, different kinds of measures are used. Colquitt (2001 ) developed a four-dimensional measure of organizational justice to allow for the comparison of different studies. Two studies provide evidence for the construct (Study 1) and criteria validity (Study 2) of the German version of the Colquitt measure with regard to perceived supervisor behavior as well as employees’ attitudes and intentions. In Study 1, the measure demonstrated construct validity using a German sample of employees (N = 227) from different companies: Each dimension correlated differently with work-related dimension of supervisor behavior. To demonstrate criteria validity in Study 2 (N = 315 employees), the justice measure predicted different, theoretically linked work-related employee behaviors or attitudes (i.e., intentions to leave, job satisfaction, job stress, individual organizational citizenship behavior). Results are discussed with regard to theoretical and practical implications, intercultural differences, and future research.
Involvement of testicular growth factors in fetal Leydig cell aggregation after exposure to phthalate
in utero
Authors: Lin Han , Ge Ren-Shan , Chen Guo-Rong , Hu Guo-Xin , Dong Lei , Lian Qing-Quan , Hardy Dianne O. , Sottas Chantal M. , Li Xiao-Kun , Hardy Matthew P.
Published: May 2008

Exposures to di-(2-ethylhexyl) phthalate (DEHP) have been shown to be associated with decreased adult testosterone (T) levels and increased Leydig cell numbers. As yet, little is known about DEHP effects
in utero
on fetal Leydig cells (FLC). The present study investigated effects of DEHP on FLC function. Pregnant Long–Evans female rats received vehicle (corn oil) or DEHP at 10, 100, or 750 mg/kg by oral gavage from gestational day (GD)2–20. At GD21, T production, FLC numbers and distribution, and testicular gene expression were examined. The percentage of FLC clusters containing 6–30 cells increased in all treatment groups, with 29 ± 2% in control vs. 37 ± 3, 35 ± 3, and 56 ± 4% in rats receiving 10, 100, and 750 mg/kg DEHP, respectively. In contrast, FLC numbers were 33% and 39% lower than control after exposures to 100 and 750 mg/kg DEHP, respectively. At these doses, mRNA levels of leukemia inhibitory factor (LIF) increased. LIF was found to induce cell aggregation in FLCs
in vitro
, consistent with the hypothesis that DEHP induced FLC aggregation. Testicular T levels were doubled by the 10 mg/kg dose and halved at 750 mg/kg. The mRNA levels of IGF-1 and c-
Kit
ligand (KITL) were induced by 10 mg/kg DEHP. These results, taken together, indicate that fetal exposures to DEHP have effects on FLC number, distribution, and most importantly, steroidogenic capacity and suggest that abnormal expressions of IGF1, KITL, and LIF genes may contribute to the reproductive toxicity of phthalates.
Scaling theory for information networks
Authors: Moses Melanie E , Forrest Stephanie , Davis Alan L , Lodder Mike A , Brown James H
Published: May 2008

Networks distribute energy, materials and information to the components of a variety of natural and human-engineered systems, including organisms, brains, the Internet and microprocessors. Distribution networks enable the integrated and coordinated functioning of these systems, and they also constrain their design. The similar hierarchical branching networks observed in organisms and microprocessors are striking, given that the structure of organisms has evolved via natural selection, while microprocessors are designed by engineers. Metabolic scaling theory (MST) shows that the rate at which networks deliver energy to an organism is proportional to its mass raised to the 3/4 power. We show that computational systems are also characterized by nonlinear network scaling and use MST principles to characterize how information networks scale, focusing on how MST predicts properties of clock distribution networks in microprocessors. The MST equations are modified to account for variation in the size and density of transistors and terminal wires in microprocessors. Based on the scaling of the clock distribution network, we predict a set of trade-offs and performance properties that scale with chip size and the number of transistors. However, there are systematic deviations between power requirements on microprocessors and predictions derived directly from MST. These deviations are addressed by augmenting the model to account for decentralized flow in some microprocessor networks (e.g. in logic networks). More generally, we hypothesize a set of constraints between the size, power and performance of networked information systems including transistors on chips, hosts on the Internet and neurons in the brain.
A quantum chemical dialogue mediated by textbooks: Pauling's
The nature of the chemical bond
and Coulson's
Valence
Authors: Simões Ana
Published: May 2008

In this paper I look at Coulson's
Valence
not as the textbook that ended the hegemonic reign of Pauling's
The nature of the chemical bond
, but as the outcome of an ongoing conversation, either literal or metaphorical, between Pauling and Coulson, in which each scientist was responding to the other, agreeing or disagreeing with him, in the process revising his ideas, and writing the successive editions of his textbook. Far from merely expository devices, these textbooks were central pieces in an intellectual dialogue involving their authors about scientific theories and the status of concepts and, to a certain extent, about their competing philosophies of science.
Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry
Authors: Mentel Marek , Martin William
Published: May 2008

Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time fromca2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fuelling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.
When did oxygenic photosynthesis evolve?
Authors: Buick Roger
Published: May 2008

The atmosphere has apparently been oxygenated since the ‘Great Oxidation Event’
ca
2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in
ca
2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as
ca
2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at
ca
3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U–Pb data from
ca
3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.
Signals Derived fromYABBYGene Activities in Organ Primordia Regulate Growth and Partitioning ofArabidopsisShoot Apical Meristems
Authors: Goldshmidt Alexander , Alvarez John Paul , Bowman John L. , Eshed Yuval
Published: May 2008

Shoot apical meristems (SAMs) are self-sustaining groups of cells responsible for the ordered initiation of all aerial plant tissues, including stems and lateral organs. The precise coordination of these processes argues for crosstalk between the different SAM domains. The products of YABBY (YAB) genes are limited to the organ primordium domains, which are situated at the periphery of all SAMs and which are separated by a margin of three to seven cells from the central meristem zone marked by WUSCHEL and CLAVATA3 expression. Mutations in the two related YAB1 genes, FILAMENTOUS FLOWER and YABBY3 (YAB3), cause an array of defects, including aberrant phyllotaxis. We show that peripheral YAB1 activity nonautonomously and sequentially affects the phyllotaxis and growth of subsequent primordia and coordinates the expression of SAM central zone markers. These effects support a role for YAB1 genes in short-range signaling. However, no evidence was found that YAB1 gene products are themselves mobile. A screen for suppression of a floral YAB1 overexpression phenotype revealed that the YAB1-born signals are mediated in part by the activity of LATERAL SUPPRESSOR. This GRAS protein is expressed at the boundary of organ primordia and the SAM central zone, distinct from the YAB1 expression domain. Together, these results suggest that YAB1 activity stimulates signals from the organs to the meristem via a secondary message or signal cascade, a process essential for organized growth of the SAM.
A Mutant Impaired in the Production of Plastome-Encoded Proteins Uncovers a Mechanism for the Homeostasis of Isoprenoid Biosynthetic Enzymes inArabidopsisPlastids
Authors: Flores-Pérez Úrsula , Sauret-Güeto Susanna , Gas Elisabet , Jarvis Paul , Rodríguez-Concepción Manuel
Published: May 2008

The plastid-localized methylerythritol phosphate (MEP) pathway synthesizes the isoprenoid precursors for the production of essential photosynthesis-related compounds and hormones. We have identified an Arabidopsis thaliana mutant, rif1, in which posttranscriptional upregulation of MEP pathway enzyme levels is caused by the loss of function of At3g47450, a gene originally reported to encode a mitochondrial protein related to nitric oxide synthesis. However, we show that nitric oxide is not involved in the regulation of the MEP pathway and that the encoded protein is a plastid-targeted homolog of the Bacillus subtilis YqeH protein, a GTPase required for proper ribosome assembly. Consistently, in rif1 seedlings, decreased levels of plastome-encoded proteins were observed, with the exception of ClpP1, a catalytic subunit of the plastidial Clp protease complex. The unexpected accumulation of ClpP1 in plastids with reduced protein synthesis suggested a compensatory mechanism in response to decreased Clp activity levels. In agreement, a negative correlation was found between Clp protease activity and MEP pathway enzyme levels in different experiments, suggesting that Clp-mediated degradation of MEP pathway enzymes might be a mechanism used by individual plastids to finely adjust plastidial isoprenoid biosynthesis to their functional and physiological states.
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions
Authors: Yang Yuedong , Zhou Yaoqi
Published: May 2008

One of the common methods for assessing energy functions of proteins is selection of native or near‐native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all‐atom statistical energy functions, DFIRE (distance‐scaled, finite, ideal‐gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence‐position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short‐range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 Å global root‐mean‐squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.
Cooperativity of complex salt bridges
Authors: Gvritishvili Anzor G. , Gribenko Alexey V. , Makhatadze George I.
Published: May 2008

The energetic contribution of complex salt bridges, in which one charged residue (anchor residue) forms salt bridges with two or more residues simultaneously, has been suggested to have importance for protein stability. Detailed analysis of the net energetics of complex salt bridge formation using double‐ and triple‐mutant cycle analysis revealed conflicting results. In two cases, it was shown that complex salt bridge formation is cooperative, i.e., the net strength of the complex salt bridge is more than the sum of the energies of individual pairs. In one case, it was reported that complex salt bridge formation is anti‐cooperative. To resolve these different findings, we performed analysis of the geometries of salt bridges in a representative set of structures from the PDB and found that over 87% of all complex salt bridges anchored by Arg/Lys have a geometry such that the angle formed by their Cα atoms, Θ, is <90°. This preferred geometry is observed in the two reported instances when the energetics of complex salt bridge formation is cooperative, while in the reported anti‐cooperative complex salt bridge, Θ is close to 160°. Based on these observations, we hypothesized that complex salt bridges are cooperative for Θ < 90° and anti‐cooperative for 90° < Θ < 180°. To provide a further experimental test for this hypothesis, we engineered a complex salt bridge with Θ = 150° into a model protein, the activation domain of human procarboxypeptidase A2 (ADA2h). Experimentally derived stabilities of the ADA2h variants allowed us to show that the complex salt bridge in ADA2h is anti‐cooperative.
Central control of thermogenesis in mammals
Authors: Morrison Shaun F. , Nakamura Kazuhiro , Madden Christopher J.
Published: May 2008

Thermogenesis, the production of heat energy, is an essential component of the homeostatic repertoire to maintain body temperature in mammals and birds during the challenge of low environmental temperature and plays a key role in elevating body temperature during the febrile response to infection. The primary sources of neurally regulated metabolic heat production are mitochondrial oxidation in brown adipose tissue, increases in heart rate and shivering in skeletal muscle. Thermogenesis is regulated in each of these tissues by parallel networks in the central nervous system, which respond to feedforward afferent signals from cutaneous and core body thermoreceptors and to feedback signals from brain thermosensitive neurons to activate the appropriate sympathetic and somatic efferents. This review summarizes the research leading to a model of the feedforward reflex pathway through which environmental cold stimulates thermogenesis and discusses the influence on this thermoregulatory network of the pyrogenic mediator, prostaglandin E2, to increase body temperature. The cold thermal afferent circuit from cutaneous thermal receptors ascends via second‐order thermosensory neurons in the dorsal horn of the spinal cord to activate neurons in the lateral parabrachial nucleus, which drive GABAergic interneurons in the preoptic area to inhibit warm‐sensitive, inhibitory output neurons of the preoptic area. The resulting disinhibition of thermogenesis‐promoting neurons in the dorsomedial hypothalamus and possibly of sympathetic and somatic premotor neurons in the rostral ventromedial medulla, including the raphe pallidus, activates excitatory inputs to spinal sympathetic and somatic motor circuits to drive thermogenesis.
Local metabolite accumulation augments passive muscle stretch‐induced modulation of carotid–cardiac but not carotid–vasomotor baroreflex sensitivity in man
Authors: Drew Rachel C. , McIntyre David B. , Ring Christopher , White Michael J.
Published: May 2008

We examined the effects of muscle mechanoreflex stimulation by passive calf muscle stretch, at rest and during concurrent muscle metaboreflex activation, on carotid baroreflex (CBR) sensitivity. Twelve subjects either performed 1.5 min one‐legged isometric plantarflexion at 50% maximal voluntary contraction with their right or left calf [two ischaemic exercise (IE) trials, IER and IEL] or rested for 1.5 min [two ischaemic control (IC) trials, ICR and ICL]. Following exercise, blood pressure elevation was partly maintained by local circulatory occlusion (CO). 3.5 min of CO was followed by 3 min of CO with passive stretch (STR‐CO) of the right calf in all trials. Carotid baroreflex function was assessed using rapid pulses of neck pressure from +40 to −80 mmHg. In all IC trials, stretch did not alter maximal gain of carotid–cardiac (CBR–HR) and carotid–vasomotor (CBR–MAP) baroreflex function curves. The CBR–HR curve was reset without change in maximal gain during STR‐CO in the IEL trial. However, during the IER trial maximal gain of the CBR–HR curve was smaller than in all other trials (−0.34 ± 0.04 beats min−1 mmHg−1 in IER versus−0.76 ± 0.20, −0.94 ± 0.14 and −0.66 ± 0.18 beats min−1 mmHg−1 in ICR, IEL and ICL, respectively), and significantly smaller than in IEL (P < 0.05). The CBR–MAP curves were reset from CO values by STR‐CO in the IEL and IER trials with no changes in maximal gain. These results suggest that metabolite sensitization of stretch‐sensitive muscle mechanoreceptive afferents modulates baroreflex control of heart rate but not blood pressure.
Variation in the human lectin‐like oxidized low‐density lipoprotein receptor 1 (LOX‐1) gene is associated with plasma soluble LOX‐1 levels
Authors: Brinkley Tina E. , Kume Noriaki , Mitsuoka Hirokazu , Brown Michael D. , Phares Dana A. , Ferrell Robert E. , Kita Toru , Hagberg James M.
Published: May 2008

The lectin‐like oxidized low‐density lipoprotein receptor 1 (LOX‐1) expressed on vascular cells plays a major role in atherogenesis by internalizing and degrading oxidized low‐density lipoprotein. LOX‐1 can be cleaved from the cell surface and released as soluble LOX‐1 (sLOX‐1), and elevated sLOX‐1 levels may be indicative of atherosclerotic plaque instability. We examined associations between the LOX‐1 gene 3′UTR‐C/T and G501C polymorphisms and plasma sLOX‐1 levels in 97 healthy older men and women. The frequencies for the 3′UTR‐T and 501C alleles were 46 and 10%, respectively. Plasma sLOX‐1 levels were significantly higher in the 3′UTR CC genotype group compared with both the CT (P= 0.02) and TT genotype groups (P= 0.002). Plasma sLOX‐1 levels were also significantly higher in the 501GC genotype group compared with the GG genotype group (P= 0.004). In univariate analyses, sLOX‐1 levels were significantly associated with both the 3′UTR‐C/T and G501C polymorphisms. These associations remained significant after adjusting for age, sex, race and body mass index. In conclusion, variation in the LOX‐1 gene is associated with plasma sLOX‐1 levels in older men and women.
Phosphorus Availability Influences Elemental Uptake in the Mycorrhizal Fungus
Glomus intraradices
, as Revealed by Particle-Induced X-Ray Emission Analysis
Authors: Olsson Pål Axel , Hammer Edith C. , Wallander Håkan , Pallon Jan
Published: May 2008

We investigated element accumulation in the arbuscular mycorrhizal fungus
Glomus intraradices
. Fungal spores and mycelia growing in monoxenic cultures were analyzed. The elemental composition was quantified using particle-induced X-ray emission (PIXE) in combination with scanning transmission ion microscopy. In the spores, Ca and Fe were associated mainly with the spore wall, while P and K showed patchy distributions and their concentrations were correlated. Excess of P in the hyphal growth medium increased the P and Si concentrations in spores and increased the K/Ca ratio in spores. Increased P availability decreased the concentration of Zn and Mn in spores. We concluded that the availability of P influences the uptake and accumulation of several elements in spores. It is demonstrated that PIXE analysis is a powerful tool for quantitative analysis of elemental accumulation in fungal mycelia.
Monitoring Bacterial Diversity of the Marine Sponge
Ircinia strobilina
upon Transfer into Aquaculture
Authors: Mohamed Naglaa M. , Rao Venkateswara , Hamann Mark T. , Kelly Michelle , Hill Russell T.
Published: May 2008

Marine sponges in the genus
Ircinia
are known to be good sources of secondary metabolites with biological activities. A major obstacle in the development of sponge-derived metabolites is the difficulty in ensuring an economic, sustainable supply of the metabolites. A promising strategy is the ex situ culture of sponges in closed or semiclosed aquaculture systems. In this study, the marine sponge
Ircinia strobilina
(order Dictyoceratida: family Irciniidae) was collected from the wild and maintained for a year in a recirculating aquaculture system. Microbiological and molecular community analyses were performed on freshly collected sponges and sponges maintained in aquaculture for 3 months and 9 months. Chemical analyses were performed on wild collected sponges and individuals maintained in aquaculture for 3 months and 1 year. Denaturing gradient gel electrophoresis was used to assess the complexity of and to monitor changes in the microbial communities associated with
I. strobilina
. Culture-based and molecular techniques showed an increase in the
Bacteroidetes
and
Alpha
- and
Gammaproteobacteria
components of the bacterial community in aquaculture. Populations affiliated with
Beta
- and
Deltaproteobacteria
,
Clostridia
, and
Planctomycetes
emerged in sponges maintained in aquaculture. The diversity of bacterial communities increased upon transfer into aquaculture.
Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Marine Planktonic Diatom
Chaetoceros tenuissimus
Meunier
Authors: Shirai Yoko , Tomaru Yuji , Takao Yoshitake , Suzuki Hidekazu , Nagumo Tamotsu , Nagasaki Keizo
Published: May 2008

Diatoms are important components of the biological community and food web in the aquatic environment. Here, we report the characteristics of a single-stranded RNA (ssRNA) virus (CtenRNAV01) that infects the marine diatom
Chaetoceros tenuissimus
Meunier (Bacillariophyceae). The ca. 31-nm virus particle is icosahedral and lacks a tail. CtenRNAV01 forms crystalline arrays occupying most of the infected host's cytoplasm. By growth experiments, the lytic cycle and the burst size were estimated to be <24 h and ∼1 × 10
4
infectious units per host cell, respectively. Stationary-phase
C. tenuissimus
cultures were shown to be more sensitive to CtenRNAV01 than logarithmic-phase cultures. The most noticeable feature of this virus is its exceptionally high yields of ∼10
10
infectious units ml
−1
; this is much higher than those of any other algal viruses previously characterized. CtenRNAV01 has two molecules of ssRNA of approximately 8.9 and 4.3 kb and three major proteins (33.5, 31.5, and 30.0 kDa). Sequencing of the total viral genome has produced only one large contig [9,431 bases excluding the poly(A) tail], suggesting considerable overlapping between the two RNA molecules. The monophyly of CtenRNAV01 compared to another diatom-infecting virus,
Rhizosolenia setigera
RNA virus, was strongly supported in a maximum likelihood phylogenetic tree constructed based on the concatenated amino acid sequences of the RNA-dependent RNA polymerase domains. Although further analysis is required to determine the detailed classification and nomenclature of this virus, these data strongly suggest the existence of a diatom-infecting ssRNA virus group in natural waters.
Response of
Sinorhizobium meliloti
to Elevated Concentrations of Cadmium and Zinc
Authors: Rossbach Silvia , Mai Danielle J. , Carter Eric L. , Sauviac Laurent , Capela Delphine , Bruand Claude , de Bruijn Frans J.
Published: May 2008

Whole-genome transcriptional profiling was used to identify genes in
Sinorhizobium meliloti
1021 that are differentially expressed during exposure to elevated concentrations of cadmium and zinc. Mutant strains with insertions in metal-regulated genes and in genes encoding putative metal efflux pumps were analyzed for their metal sensitivities, revealing a crucial role for the SMc04128-encoded P-type ATPase in the defense of
S. meliloti
against cadmium and zinc stress.
Involvement of Fumarase C and NADH Oxidase in Metabolic Adaptation ofPseudomonas fluorescensCells Evoked by Aluminum and Gallium Toxicity
Authors: Chenier Daniel , Beriault Robin , Mailloux Ryan , Baquie Mathurin , Abramia Gia , Lemire Joseph , Appanna Vasu
Published: May 2008

Iron (Fe) is a critical element in all aerobic organisms as it participates in a variety of metabolic networks. In this study, aluminum (Al) and gallium (Ga), two Fe mimetics, severely impeded the ability of the soil microbePseudomonas fluorescensto perform oxidative phosphorylation. This was achieved by disrupting the activity and expression of complexes I, II, and IV. These toxic metals also inactivated aconitase (ACN) and fumarase A (FUM A), two tricarboxylic acid cycle enzymes dependent on Fe for their catalytic activity, while FUM C, an Fe-independent enzyme, displayed an increase in activity and expression under these stressed situations. Furthermore, in the Al- and Ga-exposed cells, the activity and expression of an H2O-forming NADH oxidase were markedly increased. The incubation of the Al- and Ga-challenged cells in an Fe-containing medium led to the recovery of the affected enzymatic activities. Taken together, these data provide novel insights into how environmental pollutants such as Al and Ga interfere with cellular Fe metabolism and also illustrate the ability ofPseudomonas fluorescensto modulate metabolic networks to combat this situation.
Eukaryotic Diversity in an Anaerobic Aquifer Polluted with Landfill Leachate
Authors: Brad Traian , Braster Martin , van Breukelen Boris M. , van Straalen Nico M. , Röling Wilfred F. M.
Published: May 2008

Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of theBasidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellateHeteromita globosa(Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 102to 103cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.
Increased Respiration in the
sch9Δ
Mutant Is Required for Increasing Chronological Life Span but Not Replicative Life Span
Authors: Lavoie Hugo , Whiteway Malcolm
Published: May 2008

Loss of the protein kinase Sch9p increases both the chronological life span (CLS) and the replicative life span (RLS) of
Saccharomyces cerevisiae
by mimicking calorie restriction, but the physiological consequences of
SCH9
deletion are poorly understood. By transcriptional profiling of an
sch9Δ
mutant, we show that mitochondrial electron transport chain genes are upregulated. Accordingly, protein levels of electron transport chain subunits are increased and the oxygen consumption rate is enhanced in the
sch9Δ
mutant. Deletion of
HAP4
and
CYT1
, both of which are essential for respiration, revert the
sch9Δ
mutant respiratory rate back to a lower-than-wild-type level. These alterations of the electron transport chain almost completely blocked CLS extension by the
sch9Δ
mutation but had a minor impact on the RLS.
SCH9
thus negatively regulates the CLS and RLS through inhibition of respiratory genes, but a large part of its action on life span seems to be respiration independent and might involve increased resistance to stress. Considering that
TOR1
deletion also increases respiration and that Sch9p is a direct target of TOR signaling, we propose that
SCH9
is one of the major effectors of TOR repression of respiratory activity in glucose grown cells.
Abnormal Micronuclear Telomeres Lead to an Unusual Cell Cycle Checkpoint and Defects in
Tetrahymena
Oral Morphogenesis
Authors: Kirk Karen E. , Christ Christina , McGuire Jennifer M. , Paul Arun G. , Vahedi Mithaq , Stuart Kathleen R. , Cole Eric S.
Published: May 2008

Telomere mutants have been well studied with respect to telomerase and the role of telomere binding proteins, but they have not been used to explore how a downstream morphogenic event is related to the mutated telomeric DNA. We report that alterations at the telomeres can have profound consequences on organellar morphogenesis. Specifically, a telomerase RNA mutation termed
ter1-43AA
results in the loss of germ line micronuclear telomeres in the binucleate protozoan
Tetrahymena thermophila.
These cells also display a micronuclear mitotic arrest, characterized by an extreme delay in anaphase with an elongated, condensed chromatin and a mitotic spindle apparatus. This anaphase defect suggests telomere fusions and consequently a spindle rather than a DNA damage checkpoint. Most surprisingly, these mutants exhibit unique, dramatic defects in the formation of the cell's oral apparatus. We suggest that micronuclear telomere loss leads to a “dynamic pause” in the program of cortical development, which may reveal an unusual cell cycle checkpoint.
The CI Repressors of Shiga Toxin-Converting Prophages Are Involved in Coinfection of
Escherichia coli
Strains, Which Causes a Down Regulation in the Production of Shiga Toxin 2
Authors: Serra-Moreno R. , Jofre J. , Muniesa M.
Published: May 2008

Shiga toxins (Stx) are the main virulence factors associated with a form of
Escherichia coli
known as Shiga toxin-producing
E. coli
(STEC). They are encoded in temperate lambdoid phages located on the chromosome of STEC. STEC strains can carry more than one prophage. Consequently, toxin and phage production might be influenced by the presence of more than one Stx prophage on the bacterial chromosome. To examine the effect of the number of prophages on Stx production, we produced
E. coli
K-12 strains carrying either one Stx2 prophage or two different Stx2 prophages. We used recombinant phages in which an antibiotic resistance gene (
aph
,
cat
, or
tet
) was incorporated in the middle of the Shiga toxin operon. Shiga toxin was quantified by immunoassay and by cytotoxicity assay on Vero cells (50% cytotoxic dose). When two prophages were inserted in the host chromosome, Shiga toxin production and the rate of lytic cycle activation fell. The
c
I repressor seems to be involved in incorporation of the second prophage. Incorporation and establishment of the lysogenic state of the two prophages, which lowers toxin production, could be regulated by the CI repressors of both prophages operating in
trans
. Although the sequences of the
c
I genes of the phages studied differed, the CI protein conformation was conserved. Results indicate that the presence of more than one prophage in the host chromosome could be regarded as a mechanism to allow genetic retention in the cell, by reducing the activation of lytic cycle and hence the pathogenicity of the strains.