bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
Authors: Chen Hong-Chu , Lee Hsiao-Ching , Lin Tsai-Yun , Li Wen-Hsiung , Chen Bor-Sen 
Published: March 2004

Abstract
Motivation: Genome-wide gene expression programs have been monitored and analyzed in the yeast Saccharomyces cerevisiae, but how cells regulate global gene expression programs in response to environmental changes is still far from being understood. We present a systematic approach to quantitatively characterize the transcriptional regulatory network of the yeast cell cycle. For the interpretative purpose, 20 target genes were selected because their expression patterns fluctuated in a periodic manner concurrent with the cell cycle and peaked at different phases. In addition to the most significant five possible regulators of each specific target gene, the expression pattern of each target gene affected by synergy of the regulators during the cell cycle was characterized. Our first step includes modeling the dynamics of gene expression and extracting the transcription rate from a time-course microarray data. The second step embraces finding the regulators that possess a high correlation with the transcription rate of the target gene, and quantifying the regulatory abilities of the identified regulators.
Results: Our network discerns not only the role of the activator or repressor for each specific regulator, but also the regulatory ability of the regulator to the transcription rate of the target gene. The highly coordinated regulatory network has identified a group of significant regulators responsible for the gene expression program through the cell cycle progress. This approach may be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes.
Supplementary information: Matlab code and test data are available at http://www.ee.nthu.edu.tw/~bschen/quantitative/regulatory_network.htm
A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays
Authors: Querec Troy D. , Stoyanova Radka , Ross Eric , Patriotis Christos 
Published: March 2004

Abstract
Motivation: The radioactivity labeled DNA array platform is a robust and accurate way for a high-throughput measurement of gene expression levels in biological samples. Despite its high degree of sensitivity and reproducibility, this platform has several sources of variation. These are related to the presence of saturation effects in the array images and impede the degree of accuracy at which gene expression levels are determined.
Results: Here we describe a simple, but effective, approach for combining expression data from a series of autoradiographic exposures of variable length. This technique increases the sensitivity of this array platform by detecting low-expressed genes at longer exposures. It also improves the measurement accuracy of highly abundant genes by considering only values from the linear portion of dependency between the exposure times and gene intensities. As a result, the described approach improves the outcome of the subsequent steps of array data normalization and mining.
Defining 3D residue environment in protein structures using SCORPION and FORMIGA
Authors: Higa R. H. , Oliveira A. G. , Horita L. G. , Miura R. T. , Inoue M. K. , Kuser P. R. , Mancini A. L. , Yamagishi M. E. B. , Togawa R. C. , Neshich G. 
Published: March 2004

Abstract
Summary: Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures—SCORPION and FORMIGA—are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Cα and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite.
Availability: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org/SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS. {options: Scorpion, Formiga}
Repair-FunMap: a functional database of proteins of the DNA repair systems
Authors: Wen Liting , Feng Jin-An 
Published: March 2004

Abstract
Summary: Repair-FunMap is a functional database of the DNA repair systems. This database contains not only the proteins directly involved in DNA repair, but also the proteins that interact with the DNA repair proteins. A protein interaction network associated with the human DNA repair processes was established according to the functional relationship between proteins in the database. This network represents the current knowledge on the intrinsic signaling pathways related to DNA repair. The Repair-FunMap could become an essential resource center for cancer research, providing clues to understanding the inter-relationship between proteins in the network, and to building scientific models of the DNA repair processes.
Availability: http://astro.temple.edu/~feng/Servers/BioinformaticServers.htm
Connexin 26 and Connexin 30 Mutations in Children with Nonsyndromic Hearing Loss
Authors: Erbe Christy B. , Harris Kevin C. , Runge‐Samuelson Christina L. , Flanary Valerie A. , Wackym Phillip Ashley 
Published: March 2004

AbstractObjectives/Hypothesis Mutations in the connexin 26 (Cx26) or gap junction beta 2 gene are the leading cause of hereditary nonsyndromic sensorineural hearing loss in Caucasians. The Cx26 coding region of 68 children with nonsyndromic sensorineural hearing loss was sequenced to determine the frequency and type of Cx26 mutations in this population. Screening was also performed for a common connexin 30 (Cx30) or gap junction beta 6 mutation (del [GJB6‐D13S1830]). Children also underwent audiological testing to determine whether any correlation exists between Cx26 mutations and severity of hearing loss.Study Design In all, 68 children with nonsyndromic sensorineural hearing loss were screened for Cx26 and Cx30 mutations by polymerase chain reaction and direct sequencing.Methods Genomic DNA was amplified by polymerase chain reaction using primers that flank the entire Cx26 coding region. Screening for the 342‐kb Cx30 deletion was performed using primers that amplified the breakpoint junction of the deletion. The amplicons were then sequenced in both directions and analyzed for mutations. Audiometric testing, including pure‐tone audiometry and auditory evoked brainstem response, was also performed to determine the degree of hearing loss.Results Twenty‐seven of 68 children tested had mutations in Cx26 with 35delG being the most prevalent. Ten additional Cx26 mutations were detected including a novel compound heterozygote. Two children were heterozygous for the Cx30 del (GJB6‐D13S1830) mutation.Conclusion Cx26 and Cx30 mutations were present in 41.2% of children tested in the study population. Audiometric data supported previous studies demonstrating a greater degree of hearing loss in subjects who are homozygous for the 35delG mutation.
Protective Effect of Corticosteroid against the Cytotoxicity of Aminoglycoside Otic Drops on Isolated Cochlear Outer Hair Cells
Authors: Park Seong Kook , Choi Dukjoo , Russell Paul , John Earnest O. , Jung Timothy T. K. 
Published: March 2004

AbstractObjectives Otic drops are commonly used not only for otitis externa but also for otorrhea in the presence of tympanic membrane perforation or tympanostomy tube. Many studies demonstrated the ototoxicity of aminoglycoside. In our previous study, we observed that gentamicin (GM), when activated with liver extract, demonstrated significant cytotoxicity. The purpose of this study was to assess the protective effect of corticosteroid against the cytotoxicity of GM and tobramycin drops using isolated cochlear outer hair cells (OHCs) in vitro with liver extract.Methods OHCs from adult chinchilla cochleae were exposed to standard bathing solution, liver extract alone, and aminoglycoside otic drops with and without corticosteroid and liver extract. All experiments were performed at an osmolality of 305 ± 5 mOsm, at room temperature, and for up to 60 minutes. The images of OHCs were recorded using an inverted microscope and analyzed on the Image Pro‐Plus 3.0 program. Time to cell death and change of cell length were measured and analyzed.Results The time to cell death and percent change in cell length observed was significantly longer in the GM + liver extract + dexamethasone group than the GM + liver extract group (P < .05). The Tobradex + liver extract group showed an insignificant increase in percent change of cell length (P > .05) and significantly increased time to cell death than the tobramycin + liver extract group (P < .05).Conclusion This study demonstrated that dexamethasone significantly reduced aminoglycoside cytotoxicity.
Initiation of fungal epizootics in diamondback moth populations within a large field cage: proof of concept for auto‐dissemination
Authors: Vickers R.A. , Furlong M.J. , White A. , Pell J.K. 
Published: March 2004

AbstractAdult diamondback moths (DBM), Plutella xylostella L. (Lepidoptera: Plutellidae), inoculated with the fungus Zoophthora radicans, were released within a large field cage containing DBM‐infested potted broccoli plants. Larvae and pupae on exposed and caged control plants were examined on five occasions over the next 48 days for evidence of Z. radicans infection. Infected larvae were first detected on exposed plants 4 days after the initial release of adults, and after 48 days the infection level reached 79%. Aerially borne conidia were a factor in transmission of the fungus. Infection had no effect on possible losses of larval and adult cadavers due to scavengers in field crops. In a trial to measure the influence of infection on dispersal, twice as many non‐infected as infected males were recaptured in pheromone traps, although the difference in cumulative catch only became significant 3 days after release of the males. In a separate experiment, when adult moths were inoculated with Beauveria bassiana conidia and released into the field cage, DBM larvae collected from 37 of 96 plants sampled 4 days later subsequently died from B. bassiana infection. The distribution of plants from which the infected larvae were collected was random, but the distribution of infected larvae was clustered within the cage. These findings suggest that the auto‐dissemination of fungal pathogens may be a feasible strategy for DBM control, provided that epizootics can be established and maintained when DBM population densities are low.
Impact of competition on sex allocation by Trichogramma
Authors: Martel V. , Boivin G. 
Published: March 2004

AbstractHymenopteran parasitoids change their sex ratio following different factors. One of these factors is the exploitation of a host patch by several females. The Local Mate Competition (LMC) model (Hamilton, 1967) states that when there are many foundresses on a patch, they should lay a higher sex ratio. The impact of both intra‐ and interspecific competition on sex allocation was measured in two egg parasitoids, Trichogramma minutum Riley and T. pintoi Voegele (Hymenoptera: Trichogrammatidae), by comparing the sex ratio deposited by females exploiting host patches alone and in groups. Results showed that the sex ratio deposited by both species was higher when in groups, as predicted by the LMC model. When the sex ratio produced was compared between females either alone or in interspecific groups, T. minutum females deposited the same sex ratio, while T. pintoi produced more sons when in interspecific groups than when alone. These results are discussed following their natural habitat and their discrimination abilities.
Predicting the temperature‐dependent natural population expansion of the western corn rootworm, Diabrotica virgifera
Authors: Hemerik Lia , Busstra Cora , Mols Peter 
Published: March 2004

AbstractThe western corn rootworm, Diabrotica virgifera virgifera Leconte (Coleoptera: Chrysomelidae), was accidentally introduced near Belgrade in Serbia just before 1992 and from there its expansion into Europe started. We have estimated its mean rate of expansion from 1992 to 2000 to be approximately 33 km year−1, using data from the annual surveys of the European and Mediterranean Plant Protection Organisation.We investigated whether or not D. virgifera can establish itself at certain places in Europe, taking its temperature‐dependent development into account. We also estimated the time it will take D. virgifera to reach the Netherlands, considering only its dispersal by flight. All life stage transitions of D. virgifera were simulated with the program INSIM to assess whether or not it could establish itself in particular places. In the simulations, we used the available laboratory data on its life history characteristics, as well as a time series (2–6 years) of daily minimum and maximum temperatures from weather stations across Europe. The temperature‐dependent net reproduction resulting from the simulations showed that D. virgifera populations cannot establish themselves at latitudes above 55°N.The overall expected velocity of D. virgifera's range expansion was computed with van den Bosch et al.'s formula [van den Bosch F, Hengeveld R & Metz JAJ (1992) Analysing the velocity of animal range expansion. Journal of Biogeography 19: 135–150], where the expansion velocity was based on dispersal characteristics and demographic parameters. We predicted that D. virgifera will not reach the Netherlands by flight from the border of its 2000 range before 2018 using this overall expected velocity. The explanation of this late arrival is that the velocity of population expansion decreases in all directions from the centre of its 2000 range due to unfavourable temperatures.Our analysis is an improvement on former analyses in that it uses temperature‐dependent life history characteristics. We stress, however, that the lack of knowledge on dispersal behaviour and on the values of life history characteristics in field situations might severely limit the applicability of the predicted velocity.
Olfactory response by the aphidophagous gall midge, Aphidoletes aphidimyza to honeydew from green peach aphid, Myzus persicae
Authors: Choi Man‐Young , Roitberg Bernard D. , Shani Arnon , Raworth David A. , Lee Geon‐Hwui 
Published: March 2004

AbstractFemale adults of the aphidopagous gall midge, Aphidoletes aphidimyza (Rondani) (Diptera: Cecidomyiidae), showed an olfactory response to honeydew excreted by the green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae) under laboratory conditions. The response was only elicited by treatments with honeydew, whereas aphids, aphids with pepper plants or leaves, and pepper plants or leaves were not attractive to the midges. Dose‐dependent responses were observed from whole honeydew, honeydew volatiles extracted in pentane, and honeydew volatiles captured on Porapak Q®. When honeydew was eluted with three sequential pentane washes, a positive response was only observed from the midges for the first wash. Female midges laid more eggs on pepper plants infested with higher densities of M. persicae. The olfactory response of midges to honeydew is discussed with respect to prey location.
Colorado potato beetle control by application of the entomopathogenic nematode Heterorhabditis marelata and potato plant alkaloid manipulation
Authors: Armer Christine A. , Berry Ralph E. , Reed Gary L. , Jepsen Sarina J. 
Published: March 2004

AbstractControl of the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae), with the entomopathogenic nematode Heterorhabditis marelata Liu and Berry (Nematoda: Heterorhabditidae) was examined in the laboratory and in potato fields in north central Oregon. This research tested the hypothesis that varying nitrogen fertilizer levels would affect foliar alkaloid levels, which would stress the host, and allow increased nematode reproduction and long‐term control of the CPB. Laboratory results indicated that nematodes tended to reproduce more readily in CPB fed on potato plants with high levels of fertilizer. Field trials tested CPB population responses to four treatments: application of nematodes vs. no nematodes, with application of low vs. high rates of nitrogen fertilizer. The higher nitrogen application rate increased field foliar levels of the alkaloids solanine by 35%, and chaconine by 41% over the season. Nematodes were applied twice during the season, causing a 50% reduction in adult CPB populations, and producing six times as many dead prepupae in nematode‐treated soil samples as in the untreated samples. However, no reproducing nematodes were found in the 303 dead prepupae and pupae collected from nematode‐treated plots. Nitrogen fertilizer levels, and their related alkaloid levels, did not affect nematode infection rates or reproduction in the field. Foliar alkaloid levels of plants from the growth chamber were 3–6‐fold as high as those in the field, which may explain the variation in nematode response to nitrogen applications to host plants of the CPB. Heterorhabditis marelata is effective for controlling CPB in the field, and does not have negative non‐target effects on one of the most common endemic CPB control agents, Myiopharus doryphorae (Riley) (Diptera: Tachinidae), but the low rate of nematode reproduction cannot be manipulated through alkaloid stress to the beetle. Until H. marelata can be mass‐produced in an inexpensive manner, it will not be a commercially viable control for CPB.
Wolbachia infection and an all‐female trait in Ostrinia orientalis and Ostrinia zaguliaevi
Authors: Kageyama D. , Nishimura G. , Ohno S. , Takanashi T. , Hoshizaki S. , Ishikawa Y. 
Published: March 2004

AbstractSex ratio distortion toward females (SR trait), induced by a Wolbachia bacterium, has been reported in two species of the Ostrinia furnacalis group, viz., O. furnacalis, and O. scapulalis (Lepidoptera: Crambidae). In addition, an SR trait caused by abacterial, unidentified agent(s) is known in O. scapulalis. Here we examined the SR trait in four other species of the furnacalis group, viz., O. orientalis, O. zaguliaevi, and O. zealis from Japan, and O. nubilalis from central and eastern Europe. Wolbachia infection was detected in three O. orientalis females and in one O. zaguliaevi female, and the infection was always associated with the SR trait. In terms of wsp and ftsZ gene sequences, Wolbachia strains in O. orientalis and O. zaguliaevi were indistinguishable from each other, or from those in O. furnacalis and O. scapulalis. These findings suggest that Wolbachia strains in the four Ostrinia species are probably identical. In addition, one O. zealis female, which was negative in diagnostic PCRs for Wolbachia and general bacteria, produced an all‐female brood. This trait was very similar to the SR trait caused by abacterial agent(s) in O. scapulalis.
Nuclear factor‐κB does not mediate the inhibitory effects of dexamethasone on granulocyte–macrophage colony‐stimulating factor expression
Authors: Bergmann Martin W. , Staples Karl J. , Barnes Peter J. , Newton Robert 
Published: March 2004

SummaryHuman granulocyte–macrophage colony‐stimulating factor (GM‐CSF) reporter constructs containing up to 3·3 kb of upstream promoter sequence were transiently transfected into both Jurkat and HUT78 human T‐cell lines. In Jurkat cells, stimulation with phorbol 12‐myristate 13‐acetate (PMA) plus phytohemaglutinin (PHA) produced robust increases in reporter activity, whereas HUT78 cells showed low levels of reporter induction attributable to constitutive nuclear factor (NF)‐κB activity. Following mutation of either the proximal NF‐κB site (−85/−76) or the activator protein1 (AP‐1) motif within the conserved lymphokine element 0 (CLE0) site (−54/−31), reporter activity was markedly reduced in both cell lines. Despite this dependence on NF‐κB and CLE0/AP‐1, GM‐CSF reporter activity was unaffected by dexamethasone in either cell line. Similarly, an NF‐κB‐dependent reporter was also not repressed by dexamethasone, yet GM‐CSF release from HUT78 T cells was inhibited. These data therefore confirm a critical role for both NF‐κB and CLE0 sites in GM‐CSF promoter activation and indicate that NF‐κB may not mediate glucocorticoid‐dependent repression of GM‐CSF in these cells.
CD28 is not directly involved in the response of human CD3−CD56+ natural killer cells to lipopolysaccharide: a role for T cells
Authors: Goodier M. R. , Londei M. 
Published: March 2004

SummaryWe have previously shown that human CD3− CD56+ and CD3+ CD56+ cells from some individuals mount vigorous proliferative responses to lipopolysaccharide. Such responses have been blocked by the presence of cytotoxic T‐lymphocyte antigen‐4 immunoglobulin fusion protein in the cultures, implicating a role for B7‐mediated costimulation. Here we confirm this inhibition of natural killer (NK) expansion using antibodies against B7‐1 and B7‐2. We were unable to specifically detect CD28 on the surface of resting or stimulated human peripheral blood NK cells, however, in either lipopolysaccharide‐responsive or non‐responsive individuals, using a panel of four different anti‐CD28 monoclonal antibodies. T‐cell depletion from peripheral blood mononuclear cell cultures resulted in a reduction in the induction of CD25 on activated CD3− CD56hi cells and in the expansion and proliferation of CD3− CD56+ NK cells. Furthermore, reconstitution experiments using peripheral blood dendritic cells and purified NK cells demonstrated that NK expansion could only be achieved in the presence of purified T cells.
Immune profiling of leprosy and tuberculosis patients to 15‐mer peptides of Mycobacterium leprae and M. tuberculosis GroES in a BCG vaccinated area: implications for development of vaccine and diagnostic reagents
Authors: Hussain Rabia , Shahid Firdaus , Zafar Shahid , Dojki Maqboola , Dockrell Hazel M. 
Published: March 2004

Summary Mycobacterium leprae (ML) GroES has been shown to induce strong T cell responses in tuberculoid as well as in exposed healthy contacts of leprosy patients, and therefore this antigen has been the focus of study as a potential vaccine candidate. Paradoxically, we have shown that ML GroES also induces extremely high titres of IgG1 antibody in leprosy patients across the disease spectrum, a response associated with disease progression. IgG1 antibodies in leprosy also show a negative association with interferon‐γ, a critical T cell cytokine responsible for macrophage activation and intracellular killing of mycobacteria. We therefore queried if antibody and T cell responses were being evoked by different epitopes in ML GroES proteins. To address the issue of epitope recognition in mycobacterial diseases, we have analysed 16 peptides (15‐mer peptides) spanning the entire ML and M. tuberculosis GroES protein in leprosy (n = 19) and tuberculosis (n = 9) patients and healthy endemic controls (n = 8). Our analysis demonstrates clearly that the dominant peptides evokingT cell and IgG subclass antibodies were different. The target of both T and B cell responses were cross‐reactive epitopes in all groups. Differences in disease and healthy states related to the strength (mean intensity) of the T cell and antibody response. IgG1 and IgG3 antibodies were associated with disseminated disease and IgG 2 and IgG4 with disease limitation. Such comprehensive immune profiling of antigen‐specific responses is critical to understanding the disease pathogenesis and also if these reagents are to be exploited for either diagnostic or vaccine purposes.