bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Phosphopantetheinyl Transferase Homolog Is Essential for
Photorhabdus luminescens
To Support Growth and Reproduction of the Entomopathogenic Nematode
Heterorhabditis bacteriophora
Authors: Ciche Todd A. , Bintrim Scott B. , Horswill Alexander R. , Ensign Jerald C. 
Published: July 2002

ABSTRACT

The bacterium
Photorhabdus luminescens
is a symbiont of the entomopathogenic nematode
Heterorhabditis bacteriophora.
The nematode requires the bacterium for infection of insect larvae and as a substrate for growth and reproduction. The nematodes do not grow and reproduce in insect hosts or on artificial media in the absence of viable
P. luminescens
cells. In an effort to identify bacterial factors that are required for nematode growth and reproduction, transposon-induced mutants of
P. luminescens
were screened for the loss of the ability to support growth and reproduction of
H. bacteriophora
nematodes. One mutant, NGR209, consistently failed to support nematode growth and reproduction. This mutant was also defective in the production of siderophore and antibiotic activities. The transposon was inserted into an open reading frame homologous to
Escherichia coli
EntD, a 4′-phosphopantetheinyl (Ppant) transferase, which is required for the biosynthesis of the catechol siderophore enterobactin. Ppant transferases catalyze the transfer of the Ppant moiety from coenzyme A to a holo-acyl, -aryl, or -peptidyl carrier protein(s) required for the biosynthesis of fatty acids, polyketides, or nonribosomal peptides. Possible roles of a Ppant transferase in the ability of
P. luminescens
to support nematode growth and reproduction are discussed.
Genetic Requirements for Induction of Germination of Spores of
Bacillus subtilis
by Ca
2+
-Dipicolinate
Authors: Paidhungat Madan , Ragkousi Katerina , Setlow Peter 
Published: July 2002

ABSTRACT

Dormant
Bacillus subtilis
spores can be induced to germinate by nutrients, as well as by nonmetabolizable chemicals, such as a 1:1 chelate of Ca
2+
and dipicolinic acid (DPA). Nutrients bind receptors in the spore, and this binding triggers events in the spore core, including DPA excretion and rehydration, and also activates hydrolysis of the surrounding cortex through mechanisms that are largely unknown. As Ca
2+
-DPA does not require receptors to induce spore germination, we asked if this process utilizes other proteins, such as the putative cortex-lytic enzymes SleB and CwlJ, that are involved in nutrient-induced germination. We found that Ca
2+
-DPA triggers germination by first activating CwlJ-dependent cortex hydrolysis; this mechanism is different from nutrient-induced germination where cortex hydrolysis is not required for the early germination events in the spore core. Nevertheless, since nutrients can induce release of the spore's DPA before cortex hydrolysis, we examined if the DPA excreted from the core acts as a signal to activate CwlJ in the cortex. Indeed, endogenous DPA is required for nutrient-induced CwlJ activation and this requirement was partially remedied by exogenous Ca
2+
-DPA. Our findings thus define a mechanism for Ca
2+
-DPA-induced germination and also provide the first definitive evidence for a signaling pathway that activates cortex hydrolysis in response to nutrients.
Different Physiological Roles of ATP- and PPi-Dependent Phosphofructokinase Isoenzymes in the Methylotrophic ActinomyceteAmycolatopsis methanolica
Authors: Alves A. M. C. R. , Euverink G. J. W. , Santos H. , Dijkhuizen L. 
Published: July 2002

ABSTRACTCells of the actinomyceteAmycolatopsis methanolicagrown on glucose possess only a single, exclusively PPi-dependent phosphofructokinase (PPi-PFK) (A. M. C. R. Alves, G. J. W. Euverink, H. J. Hektor, J. van der Vlag, W. Vrijbloed, D.H.A. Hondmann, J. Visser, and L. Dijkhuizen, J. Bacteriol. 176:6827–6835, 1994). When this methylotrophic bacterium is grown on one-carbon (C1) compounds (e.g., methanol), an ATP-dependent phosphofructokinase (ATP-PFK) activity is specifically induced, completely replacing the PPi-PFK. The twoA. methanolicaPFK isoenzymes have very distinct functions, namely, in the metabolism of C6and C1carbon substrates. This is the first report providing biochemical evidence for the presence and physiological roles of PPi-PFK and ATP-PFK isoenzymes in a bacterium. The novel ATP-PFK enzyme was purified to homogeneity and characterized in detail at the biochemical and molecular levels. TheA. methanolicaATP-PFK and PPi-PFK proteins possess a low level of amino acid sequence similarity (24%), clearly showing that the two proteins are not the result of a gene duplication event. PPi-PFK is closely related to other (putative) actinomycete PFK enzymes. Surprisingly, theA. methanolicaATP-PFK is most similar to ATP-PFK from the protozoonTrypanosoma bruceiand PPi-PFK proteins from the bacteriaBorrelia burgdorferiandTreponema pallidum, both spirochetes, very distinct from actinomycetes. The data thus suggest thatA. methanolicaobtained the ATP-PFK-encoding gene via a lateral gene transfer event.
Prevalence of Antibodies to Hepatitis E Virus in Veterinarians Working with Swine and in Normal Blood Donors in the United States and Other Countries
Authors: Meng X. J. , Wiseman B. , Elvinger F. , Guenette D. K. , Toth T. E. , Engle R. E. , Emerson S. U. , Purcell R. H. 
Published: July 2002

ABSTRACT
Hepatitis E virus (HEV) is endemic in many developing and some industrialized countries. It has been hypothesized that animals may be the source of infection. The recent identification of swine HEV in U.S. pigs and the demonstration of its ability to infect across species have lent credence to this hypothesis. To assess the potential risk of zoonotic HEV infection, we tested a total of 468 veterinarians working with swine (including 389 U.S. swine veterinarians) and 400 normal U.S. blood donors for immunoglobulin G anti-HEV. Recombinant capsid antigens from a U.S. strain of swine HEV and from a human HEV strain (Sar-55) were each used in an enzyme-linked immunosorbent assay. The anti-HEV prevalence assayed with the swine HEV antigen showed 97% concordance with that obtained with the human HEV antigen (κ = 92%). Among the 295 swine veterinarians tested from the eight U.S. states (Minnesota, Indiana, Nebraska, Iowa, Illinois, Missouri, North Carolina, and Alabama) from which normal blood donor samples were available, 26% were positive with Sar-55 antigen and 23% were positive with swine HEV antigen. In contrast, 18% of the blood donors from the same eight U.S. states were positive with Sar-55 antigen and 17% were positive with swine HEV antigen. Swine veterinarians in the eight states were 1.51 times more likely when tested with swine HEV antigen (95% confidence interval, 1.03 to 2.20) and 1.46 times more likely when tested with Sar-55 antigen (95% confidence interval, 0.99 to 2.17) to be anti-HEV positive than normal blood donors. We did not find a difference in anti-HEV prevalence between veterinarians who reported having had a needle stick or cut and those who had not or between those who spent more time (≥80% of the time) and those who spent less time (≤20% of the time) working with pigs. Similarly, we did not find a difference in anti-HEV prevalence according to four job categories (academic, practicing, student, and industry veterinarians). There was a difference in anti-HEV prevalence in both swine veterinarians and blood donors among the eight selected states, with subjects from Minnesota six times more likely to be anti-HEV positive than those from Alabama. Age was not a factor in the observed differences from state to state. Anti-HEV prevalence in swine veterinarians and normal blood donors was age specific and paralleled increasing age. The results suggest that swine veterinarians may be at somewhat higher risk of HEV infection than are normal blood donors.
The Human Factors YY1 and LSF Repress the Human Immunodeficiency Virus Type 1 Long Terminal Repeat via Recruitment of Histone Deacetylase 1
Authors: Coull Jason J. , Romerio Fabio , Sun Jian-Min , Volker Janet L. , Galvin Katherine M. , Davie James R. , Shi Yang , Hansen Ulla , Margolis David M. 
Published: July 2002

ABSTRACT
Enigmatic mechanisms restore the resting state in activated lymphocytes following human immunodeficiency virus type 1 (HIV-1) infection, rarely allowing persistent nonproductive infection. We detail a mechanism whereby cellular factors could establish virological latency. The transcription factors YY1 and LSF cooperate in repression of transcription from the HIV-1 long terminal repeat (LTR). LSF recruits YY1 to the LTR via the zinc fingers of YY1. The first two zinc fingers were observed to be sufficient for this interaction in vitro. A mutant of LSF incapable of binding DNA blocked repression. Like other transcriptional repressors, YY1 can function via recruitment of histone deacetylase (HDAC). We find that HDAC1 copurifies with the LTR-binding YY1-LSF repressor complex, the domain of YY1 that interacts with HDAC1 is required to repress the HIV-1 promoter, expression of HDAC1 augments repression of the LTR by YY1, and the deacetylase inhibitor trichostatin A blocks repression mediated by YY1. This novel link between HDAC recruitment and inhibition of HIV-1 expression by YY1 and LSF, in the natural context of a viral promoter integrated into chromosomal DNA, is the first demonstration of a molecular mechanism of repression of HIV-1. YY1 and LSF may establish transcriptional and virological latency of HIV, a state that has recently been recognized in vivo and has significant implications for the long-term treatment of AIDS.
Induction of Necrotic-Like Cell Death by Tumor Necrosis Factor Alpha and Caspase Inhibitors: Novel Mechanism for Killing Virus-Infected Cells
Authors: Li Ming , Beg Amer A. 
Published: July 2002

ABSTRACT
Induction of apoptotic cell death generally requires the participation of cysteine proteases belonging to the caspase family. However, and similar to most cell types, mouse fibroblasts are normally resistant to tumor necrosis factor alpha (TNF-α)-induced apoptosis. Surprisingly, TNF-α treatment of vaccinia virus-infected mouse fibroblasts resulted in necrotic-like cell death, which was significantly reduced in cells infected with a vaccinia virus mutant lacking the caspase inhibitor B13R. Furthermore, TNF-α also induced necrotic-like cell death of fibroblasts in the presence of peptidyl caspase inhibitors. In both cases, necrosis was accompanied by generation of superoxide species. Caspase inhibitors also sensitized fibroblasts to killing by double-stranded RNA and gamma interferon. In all cases, cell death was efficiently blocked by antioxidants or mitochondrial respiratory chain inhibitors. These results define a new mitochondrion-dependent mechanism which may be important in the killing of cells infected with viruses encoding caspase inhibitors.
Efficient Virus Extinction by Combinations of a Mutagen and Antiviral Inhibitors
Authors: Pariente Nonia , Sierra Saleta , Lowenstein Pedro R. , Domingo Esteban 
Published: July 2002

ABSTRACT

The effect of combinations of the mutagenic base analog 5-fluorouracil (FU) and the antiviral inhibitors guanidine hydrochloride (G) and heparin (H) on the infectivity of foot-and-mouth disease virus (FMDV) in cell culture has been investigated. Related FMDV clones differing up to 10
6
-fold in relative fitness in BHK-21 cells have been compared. Systematic extinction of intermediate fitness virus was attained with a combination of FU and G but not with the mutagen or the inhibitor alone. Systematic extinction of high-fitness FMDV required the combination of FU, G, and H. FMDV showing high relative fitness in BHK-21 cells but decreased replicative ability in CHO cells behaved as a low-fitness virus with regard to extinction mutagenesis in CHO cells. This confirms that relative fitness, rather than a specific genomic sequence, determines the FMDV response to enhanced mutagenesis. Mutant spectrum analysis of several genomic regions from a preextinction population showed a statistically significant increase in the number of mutations compared with virus passaged in parallel in the absence of FU and inhibitors. Also, in a preextinction population the types of mutations that can be attributed to the mutagenic action of FU were significantly more frequent than other mutation types. The results suggest that combinations of mutagenic agents and antiviral inhibitors can effectively drive high-fitness virus into extinction.
Human T-Cell Leukemia Virus Type 1 Tax Protein Binds to Assembled Nuclear Proteasomes and Enhances Their Proteolytic Activity
Authors: Hemelaar Joris , Bex Françoise , Booth Bruce , Cerundolo Vincenzo , McMichael Andrew , Daenke Susan 
Published: July 2002

ABSTRACT
The human T-cell leukemia virus type 1 (HTLV-1) Tax protein activates the HTLV-1 long terminal repeat and key regulatory proteins involved in inflammation, activation, and proliferation and may induce cell transformation. Tax is also the immunodominant target antigen for cytotoxic T cells in HTLV-1 infection. We found that Tax bound to assembled nuclear proteasomes, but Tax could not be detected in the cytoplasm. Confocal microscopy revealed a partial colocalization of Tax with nuclear proteasomes. As Tax translocated into the nucleus very quickly after synthesis, this process probably takes place prior to and independent of proteasome association. Tax mutants revealed that both the Tax N and C termini play a role in proteasome binding. We also found that proteasomes from Tax-transfected cells had enhanced proteolytic activity on prototypic peptide substrates. This effect was not due to the induction of the LMP2 and LMP7 proteasome subunits. Furthermore, Tax appeared to be a long-lived protein, with a half-life of around 15 h. These data suggest that the association of Tax with the proteasome and the enhanced proteolytic activity do not target Tax for rapid degradation and may not determine its immunodominance.
Exercise dependence, social physique anxiety, and social support in experienced and inexperienced bodybuilders and weightlifters
Authors: Hurst Richard , Hale Bruce , Smith David , Collins David 
Published: July 2002

Objectives—To investigate psychological correlates of exercise dependence in experienced and inexperienced bodybuilders and weightlifters. Secondary objectives included measuring social physique anxiety, bodybuilding identity, and social support among bodybuilders and weightlifters.Methods—Thirty five experienced bodybuilders, 31 inexperienced bodybuilders, and 23 weightlifters completed the bodybuilding dependence scale, a bodybuilding version of the athletic identity measurement scale, the social physique anxiety scale, and an adapted version of the social support survey-clinical form.Results—A between subjects multivariate analysis of variance was calculated on the scores of the three groups of lifters for the four questionnaires. UnivariateFtests and follow up tests indicated that experienced bodybuilders scored significantly higher than inexperienced bodybuilders and weightlifters on bodybuilding dependence (p<0.001), social identity and exclusivity subscales of bodybuilding identity (p<0.001), and social support scales (p<.001), and significantly lower on social physique anxiety (p<0.001).Conclusion—Experienced bodybuilders exhibit more exercise dependence, show greater social support behaviour, and experience less social physique anxiety than inexperienced bodybuilders and weightlifters.
LOGISTIC REGRESSION MODELING OF SOFTWARE QUALITY
Authors: KHOSHGOFTAAR TAGHI M. , ALLEN EDWARD B. 
Published: July 2002

Reliable software is mandatory for complex mission-critical systems. Classifying modules as fault-prone, or not, is a valuable technique for guiding development processes, so that resources can be focused on those parts of a system that are most likely to have faults. Logistic regression offers advantages over other classification modeling techniques, such as interpretable coefficients. There are few prior applications of logistic regression to software quality models in the literature, and none that we know of account for prior probabilities and costs of misclassification. A contribution of this paper is the application of prior probabilities and costs of misclassification to a logistic regression-based classification rule for a software quality model. This paper also contributes an integrated method for using logistic regression in software quality modeling, including examples of how to interpret coefficients, how to use prior probabilities, and how to use costs of misclassifications. A case study of a major subsystem of a military, real-time system illustrates the techniques.
Analyzing bounding boxes for object intersection
Authors: Suri Subhash , Hubbard Philip M. , Hughes John F. 
Published: July 2002

Heuristics that exploit bouning boxes are common in algorithms for rendering, modeling, and animation. While experience has shown that bounding boxes improve the performance of these algorithms in practice, the previous theoretical analysis has concluded that bounding boxes perform poorly in the worst case. This paper reconciles this discrepancy by analyzing intersections amongngeometric objects in terms of two parameters: α an upper bound on theaspect ratioor elongatedness of each object; and σ an upper bound on thescale factoror size disparity between the largest and smallest objects. LettingKoandKbbe the number of intersecting object pairs and bounding box pairs, respectively, we analyze a ratio measure of the bounding boxes' efficiency, ρ =Kb/ (n + K0). The analysis proves thatρ = O(α√σlog2σ)andρ = Ω(α√σ).One important consequence is that if α and σ are small constants (as is often the case in practice), thenKb=O(Ko)+O(n, so an algorithm that uses bounding boxes has time complexity proportional to the number of actual object intersections. This theoretical result validates the efficiency that bounding boxes have demonstrated in practice. Another consequence of our analysis is a proof of the output-sensitivity of an algorithm for reporting all intersecting pairs in a set ofnconvex polyhedra with constant α and σ. The algorithm takes timeO(nlogd-1n+Kologd-1n) for dimensiond= 2, 3. This running time improves on the performance of previous algorithms, which make no assumptions about α and σ.
Understanding the effectiveness of computer graphics for decision support: a cumulative experimental approach
Authors: Dickson Gary W. , DeSanctis Gerardine , McBride D. J. 
Published: July 2002

A total of 840 junior and senior-level undergraduate business students particpated in three experiments that compared computer-generated graphical forms of data presentation to traditional tabular reports. The first experiment compared tables and bar charts for their effects on readability, interpretation accuracy, and decision making. No differences in interpretation accuracy or decision quality were observed for the two groups, although tabular reports were rated as "easier to read and understand" than graphical reports. The second experiment compared line plots to tables for their effects on interpretation accuracy and decision quality. Subjects with graphical reports outperformed those with tables. There were no meaningful differences in interpretation accuracy across treatment groups. The third experiment compared graphical and tabular reports for their ability to convey a "message" to the reader. Only in situations in which a vast amount of information was presented and relatively simple impressions were to be made, did subjects given graphs outperform those using tables.
This program of cumulative experiments indicates that generalized claims of superiority of graphic presentation are unsupported, at least for decision-related activities. In fact, the experiments suggest that the effectiveness of the data display format is largely a function of the characteristics of the task at hand, and that impressions gleaned from "one shot" studies of the effectiveness of the use of graphs may be nothing more than situationally dependent artifacts.
OXYGEN DEFICIENCY AND ROOT METABOLISM: Injury and Acclimation Under Hypoxia and Anoxia
Authors: Drew Malcolm C. 
Published: July 2002

▪ Abstract  Oxygen deficiency in the rooting zone occurs with poor drainage after rain or irrigation, causing depressed growth and yield of dryland species, in contrast with native wetland vegetation that tolerates such conditions. This review examines how roots are injured by O2 deficiency and how metabolism changes during acclimation to low concentrations of O2. In the root apical meristem, cell survival is important for the future development; metabolic changes under anoxia help maintain cell survival by generating ATP anaerobically and minimizing the cytoplasmic acidosis associated with cell death. Behind the apex, where cells are fully expanded, ethylene-dependent death and lysis occurs under hypoxia to form continuous, gas-filled channels (aerenchyma) conveying O2 from the leaves. This selective sacrifice of cells may resemble programmed cell death and is distinct from cell death caused by anoxia. Evidence concerning alternative possible mechanisms of anoxia tolerance and avoidance is presented.
HOST PLANT INFLUENCES ON SEX PHEROMONE BEHAVIOR OF PHYTOPHAGOUS INSECTS
Authors: Landolt Peter J. , Phillips Thomas W. 
Published: July 2002

▪ Abstract  The sexual behavior of phytophagous insects is often integrated in a variety of ways with their host plants. This integration may be manifested as effects or influences of host plants on insect physiology and behavior, including sex pheromone communication, that reflect strategies by insects to optimize mating and reproduction. Certain insects sequester or otherwise acquire host plant compounds and use them as sex pheromones or sex pheromone precursors. Other insects produce or release sex pheromones in response to particular host plant cues. Chemicals from host plants often synergize or otherwise enhance insect responses to sex pheromones. By these means, host plants may be used by insects to regulate or mediate sexual communication.For many species of insects, host plant influences on insect sex pheromone communication may be important aspects of the formation of feeding and mating aggregations, of insect strategies to locate both hosts and mates, of behavioral reproductive isolation among sibling species, and of the regulation of reproduction to coincide with the availability of food and oviposition sites. Knowledge of these relationships is critical to understanding many different areas of the behavioral ecology of plant-feeding insects.