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PubMed1998

Only long sperm are fertilization-competent in six sperm-heteromorphic Drosophila species.

Males of many species exhibit sperm heteromorphism, in which multiple morphologies of sperm are produced in a common testis (see references in [1]). Polymegaly, a form of sperm heteromorphism, is found in the Drosophila obscura group and is characterized by the production of two size classes of nucleated sperm that differ only in head and tail lengths [1,2]. Both the length and the ratio of sperm types produced is species-specific [1,3-5], and each sperm type develops in its own bundle deriving from a single stem cell [4]. Previous studies suggested that both types of sperm are fertilization-competent on the basis of similar ultrastructure [6], DNA content [6], nuclear protein transition during spermatogenesis [7], and storage in females [3-5]. However, a previous study demonstrated that only long sperm fertilize eggs [3]. Here, we extend this study to examine fertilization in six obscura group species using anti-sperm antibodies and digital deconvolution microscopy. Consistent with the previous study, we found that all eggs were fertilized by only the long sperm type, even in polyspermic eggs. Moreover, sperm entry and position during and following fertilization were similar to other Drosophila groups [3,8-10]. Thus, polymegaly and its maintenance appear to have arisen independently of fertilization processes per se.

Animals↗

PubMed2002

Investigation of penetratin peptides. Part 1. The environment dependent conformational properties of penetratin and two of its derivatives.

The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three alpha-helices and one beta-turn between helices II and III. Its third helix from the N-terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments: 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9: 1), on the basis of 553 distance restraints, the 4-12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both alpha-helical and 310-helical features, the structure of peptide 3 is predominantly a 310-helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment.

Amino Acid Sequence↗

PubMed2005

Occurrence and distribution of endobacteria in the plant-associated mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N.

Fluorescence in situ hybridization, associated with confocal laser scanning microscopy or epifluorescence microscopy with deconvolution system, has allowed the detection of a community of intracellular bacteria in non-axenic samples of the ectomycorrhizal fungus Laccaria bicolor S238N. The endobacteria, mainly alpha-proteobacteria, were present in more than half of the samples, which consisted of ectomycorrhizae, fungal mats and fruit bodies, collected in the glasshouse or in the forest. Acridine orange staining suggests that the endobacteria inhabit both live and dead fungal cells. The role of these endobacteria remains to be clarified.

Acridine Orange↗

PubMed2000

Mass spectrometric determination of appearance energies for ions formed from CoF(4) and CoF(3) molecules.

Knudsen cell mass spectrometry was applied to the evaluation of the ionization efficiency curves for the ions originating from CoF(4) molecules. Cobalt tetrafluoride was obtained in the gas phase over the CoF(3)(s)-TbF(4)(s) system in the temperature range from 640 to 690 K. From the ionization efficiency curves the appearance energies of the ions formed from the CoF(4) molecules were determined by means of Vogt's deconvolution method. Clausius-Clapeyron plots for the ions from CoF(4) molecules were measured. Evaporation of pure CoF(3)(s) was carried out, and the appearance energies of the ions formed from CoF(3) molecules were determined. The ionization energies for CoF(4) and CoF(3) molecules were found to be (14.3 +/- 0.2) and (13.3 +/- 0.1) eV, respectively.

Cobalt↗

PubMed2006

Correlation between initial and early follow-up CT perfusion parameters with endoscopic tumor response in patients with advanced squamous cell carcinomas of the oropharynx treated with organ-preservation therapy.

BACKGROUND AND PURPOSE: Current organ-preservation regimens for upper aerodigestive tract squamous cell carcinoma (SCCA) require endoscopic procedures under general anesthesia to evaluate the tumor response. The purpose of our study was to determine whether CT perfusion (CTP) parameters correlate with response to induction chemotherapy as assessed by endoscopy under general anesthesia. METHODS: Nine patients with advanced (stage 3 or 4) SCCA of the oropharynx were enrolled in a nested phase 2 prospective trial in which induction chemotherapy was used to assess the tumor response. Patients underwent direct laryngoscopy and CTP before and 3 weeks after one cycle of induction chemotherapy. The outcome variables were the surgeon's estimate of tumor volume during endoscopy with biopsy under anesthesia and CTP parameters (capillary permeability (CP), blood volume (BV), blood flow (BF), and mean transit time (MTT)). Wilcoxon rank sum analysis was used to correlate the baseline values of BF and BV with response to induction chemotherapy. Comparison of agreement between the reduction in tumor volume and change in CTP parameters was performed by using kappa estimates. RESULTS: Seven of 9 patients demonstrated > or =50% tumor volume reduction, representing positive response to induction chemotherapy. In the responder group, the following changes in mean pre- and postinduction chemotherapy values were noted: mean BF, 114.2 mL/100 g /min (preinduction) to 45.1 mL/100 g/min (postinduction); mean BV, 5.11 mL/100 g to 3.1 mL/100 g; mean CP, 25.6 mL/100 g /min (preinduction) to 18.3 mL/100 g / min (postinduction); mean MTT, 4.9 seconds (preinduction) to 8.0 seconds (postinduction). In the nonresponder group, the following changes were noted: mean BF, 56.9 mL/100 g/min to 75.9 mL/100 g/min; mean, BV 2.7 mL/100 g to 4.71 mL/100 g; mean CP, 24.1 mL/100 g/min to 23.7 mL/100 g/min; mean MTT, 4.3 seconds to 5.34 seconds. Higher baseline (pretherapy) values of BV showed significant correlation with endoscopic tumor response (P < .05). Reduction in the BV (by >/=20%) on follow-up studies also showed substantial agreement with clinical response as assessed with endoscopy (kappa = 0.73). The agreement between decreased BF, decreased CP, and increased MTT and clinical response was fair (kappa = 0.37). CONCLUSION: These preliminary results show that deconvolution-based CTP technique offers potential for noninvasive monitoring of response to induction chemotherapy in patients with oropharyngeal cancers. Percentage reduction of BV is significantly correlated to endoscopic response to induction chemotherapy, though we acknowledge that the data correspond to short-term outcomes and long-term durability of response cannot be established. Nevertheless, validation of the use of deconvolution CTP parameters as predictors of tumor response may permit replacement of an invasive diagnostic procedure conducted under anesthesia currently used to assess response with noninvasive perfusion CT imaging.

Aged↗

PubMed2001

Localization of the Plasmodium falciparum PfNT1 nucleoside transporter to the parasite plasma membrane.

Nutrient transporters play critical roles in parasite metabolism, but the membranes in which they reside have not been clearly defined. The transport of purine nutrients is crucial to the survival of the malaria parasite Plasmodium falciparum, and nucleoside transport activity has been associated with a number of different membrane components within the parasitized erythrocyte. To determine the location of the PfNT1 nucleoside transporter, the first component of the nucleoside permeation pathway to be studied at the molecular level in P. falciparum (Carter, N. S., Ben Mamoun, C., Liu, W., Silva, E. O., Landfear, S. M., Goldberg, D. E., and Ullman, B. (2000) J. Biol. Chem. 275, 10683-10691), polyclonal antisera against the NH2-terminal 36 amino acids of PfNT1 were raised in rabbits. Western blot analysis of parasite lysates revealed that the antibodies were specific for PfNT1 and that the level of PfNT1 protein in the infected erythrocyte is regulated in a stage-specific fashion. The amount of PfNT1 polypeptide increases dramatically during the early trophozoite stage and reaches its maximal level in the late trophozoite and schizont stages. Deconvolution and immunoelectron microscopy using these monospecific antibodies revealed that PfNT1 localizes predominantly, if not exclusively, to the plasma membrane of the parasite and not to the parasitophorous vacuolar or erythrocyte membranes.

Animals↗

PubMed2001

Deconvolution and wavelet-based methods for membrane current estimation from simulated fractionated electrograms.

In infarcted myocardium, extracellular recordings exhibit multiple deflections due to irregular pathway of the electric impulse. In this work the problem of distinguishing local from distant deflections is tackled. In order to evaluate the proposed methods in a controlled setting, simulated data are used, following both Beeler-Reuter and Luo-Rudy kinetics. The input is an array of electrograms positioned on grid-points of a rectangular grid and the output is an array of estimates of the membrane current. First, deconvolution techniques are used in the form of spatial filtering for membrane current estimation from the extracellular recordings. Second, the extracellular recordings undergo wavelet based transformation, followed by a spatial filter which enhances local activity deflections and suppresses distant activity deflections. It is shown that wavelet filtering of the extracellular recordings acts as an evaluator of the efficiency of the deconvolution techniques for the membrane current estimation. Subsequently, activation times based on the results from the two methods are used for the reconstruction of the propagation pattern in a zig-zag case in two-dimensional grids. It is shown that the wavelet-based method is more robust, and can work well even in cases where the grid interval in the y direction is four times larger than the single cell size.

Algorithms↗

PubMed1998

Identification of noncovalent dimeric complexes of the recombinant murine S100 protein CP10 by electrospray ionization mass spectrometry and chemical cross-linking.

CP10 is a chemotactic S100 protein expressed by murine myeloid cells. A specific noncovalently linked dimeric complex of recombinant Ala43 CP10 was identified after electrospray ionization mass spectrometry using a nondenaturing solvent of 5-mM ammonium acetate (pH 6.5) and source temperature of 50 degrees C. With a low cone voltage (75 V), major ions were observed at approximately 2075, 2305, and 2613 Da, which were attributed to partially desolvated multiply charged noncovalently linked dimeric species (+10, +9, and +8 charge states, respectively). Deconvolution produced a broad peak centered around 20750 Da corresponding to the approximate mass of dimeric recombinant Ala43 CP10. Increasing the cone voltage, the collisionally activating the complex, gradually reduced the intensity of these dimeric ions, with a concomitant increase in higher and lower charge state monomeric ions. The intensities of these dimeric ions were greatly reduced in spectra recorded with a source temperature of 140 degrees C and cone voltage of 75 V, indicating a thermally unstable noncovalent complex. Similar spectra were obtained using recombinant CP10. Specific noncovalent S100 dimeric complexes were confirmed by chemically cross-linking recombinant Ala43 CP10 or CP10 with bis (sulfosuccinimidyl) suberate, followed by SDS/PAGE. The dominant silver-stained and CP10-immunoreactive component migrated at 20,000 suggested that the complex represents the major isoform in solution.

Animals↗

PubMed2002

Identification of unique VLA-4 antagonists from a combinatorial library.

A combinatorial library of 28 pools of 180 compounds (345 diastereomers) was designed and prepared in support of the delineation of the SAR of two prototypical VLA-4 antagonists. Deconvolution of the active pools led to the identification of three novel series of VLA-4 antagonists with low nanomolar potencies.

Anti-Inflammatory Agents↗

PubMed2004

Upregulation and nuclear recruitment of HDAC1 in hormone refractory prostate cancer.

BACKGROUND: Histone deacetylase 1 (HDAC1) is a co-repressor involved in differentiation and proliferation control. It is upregulated in malignant compared to benign tissue, and targets a number of transcription factors including p53. METHODS: By immunohistochemistry, HDAC1 protein expression was investigated in human prostate specimens and the CWR22 mouse xenograft model. Flow cytometry and deconvolution immunofluorescence were also performed. RESULTS: HDAC1 was upregulated in pre-malignant and malignant lesions, with the highest increase in expression in hormone refractory (HR) cancer. Using the CWR22 xenograft model we showed androgen dependent regulation of HDAC1. HDAC1 overexpression led to a significant increase in proliferation and a shift towards the undifferentiated cytokeratin (CK) profile in a PC3M derivative clone constitutively expressing HDAC1. CONCLUSION: This study underlines the importance of HDAC1 in cell proliferation and the development of prostate cancer (CaP) and proposes a mechanism for HDAC1 nuclear recruitment. HDAC1 may constitute a crucial therapeutic target particularly in the most lethal phase of androgen independence.

Androgens↗

PubMed1995

Effects of aging on glucose regulation during wakefulness and sleep.

Glucose intolerance, reduced sleep efficiency, and disturbed circadian rhythmicity occur in aging. In normal young subjects, glucose regulation is modulated by sleep and circadian rhythmicity. To examine age-related alterations in the temporal pattern of glucose tolerance and insulin secretion, eight modestly overweight healthy older men, eight weight-matched young men, and six young lean men were studied during constant glucose infusion for 53 h. Levels of glucose, insulin, C-peptide, and growth hormone (GH) were measured every 20 min. Rates of insulin and GH secretion were calculated by deconvolution. In older volunteers, sleep ws shallow and more fragmented than in young subjects but was nevertheless associated with robust glucose elevations. However, postsleep increases of insulin secretion were markedly dampened. During wakefulness, the normal morning-to-evening increase in glucose was preserved in the elderly, but insulin secretion failed to increase proportionately. Thus decreased glucose tolerance in aging is associated with insulin resistance and also with a relative insensitivity of the beta-cell to the modulation of glucose regulation by sleep and circadian rhythmicity.

Adult↗

PubMed1992

Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures.

The octadeoxyribonucleotide d(CGCICICG) has been crystallized in space group P(6)5(22) with unit cell dimensions of a = b = 31.0 A and c = 43.7 A, and X-ray diffraction data have been collected to 1.5-A resolution. Precession photographs and the self-Patterson function indicate that 12 base pairs of Z-conformation DNA stack along the c-axis, and the double helices pack in a hexagonal array similar to that seen in other crystals of Z-DNA. The structure has been solved by both Patterson deconvolution and molecular replacement methods and refined in space group P(6)5 to an R factor of 0.225 using 2503 unique reflections greater than 3.0 sigma (F). Comparison of the molecules within the hexagonal lattice with highly refined crystal structures of other Z-DNA reveals only minor conformational differences, most notably in the pucker of the deoxyribose of the purine residues. The DNA has multiple occupancy of C:I and C:G base pairs, and C:I base pairs adopt a conformation similar to that of C:G base pairs.

Base Composition↗

PubMed2003

Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis.

Cells adjust gene expression profiles in response to environmental and physiological changes through a series of signal transduction pathways. Upon activation or deactivation, the terminal regulators bind to or dissociate from DNA, respectively, and modulate transcriptional activities on particular promoters. Traditionally, individual reporter genes have been used to detect the activity of the transcription factors. This approach works well for simple, non-overlapping transcription pathways. For complex transcriptional networks, more sophisticated tools are required to deconvolute the contribution of each regulator. Here, we demonstrate the utility of network component analysis in determining multiple transcription factor activities based on transcriptome profiles and available connectivity information regarding network connectivity. We used Escherichia coli carbon source transition from glucose to acetate as a model system. Key results from this analysis were either consistent with physiology or verified by using independent measurements.

Cyclic AMP↗

PubMed2000

Traffic pattern of cystic fibrosis transmembrane regulator through the early exocytic pathway.

The pathway of transport of the cystic fibrosis transmembrane regulator (CFTR) through the early exocytic pathway has not been examined. In contrast to most membrane proteins that are concentrated during export from the ER and therefore readily detectable at elevated levels in pre-Golgi intermediates and Golgi compartments, wild-type CFTR could not be detected in these compartments using deconvolution immunofluorescence microscopy. To determine the basis for this unusual feature, we analyzed CFTR localization using quantitative immunoelectron microscopy (IEM). We found that wild-type CFTR is present in pre-Golgi compartments and peripheral tubular elements associated with the cis and trans faces of the Golgi stack, albeit at a concentration 2-fold lower than that found in the endoplasmic reticulum (ER). delta F508 CFTR, a mutant form that is not efficiently delivered to the cell surface and the most common mutation in cystic fibrosis, could also be detected at a reduced concentration in pre-Golgi intermediates and peripheral cis Golgi elements, but not in post-Golgi compartments. Our results suggest that the low level of wild-type CFTR in the Golgi region reflects a limiting step in selective recruitment by the ER export machinery, an event that is largely deficient in delta F508. We raise the possibility that novel modes of selective anterograde and retrograde traffic between the ER and the Golgi may serve to regulate CFTR function in the early secretory compartments.

Animals↗

PubMed2000

Augmentation of alimentary insulin secretion despite similar gastric inhibitory peptide (GIP) responses in juvenile obesity.

Insulin secretion rates are greater after oral glucose than after parenteral administration of an equivalent glucose load. This augmented beta-cell secretory response to an oral glucose load results from the release of mainly two gut hormones: gastric inhibitory polypeptide (GIP) and glucagon-like peptide-1, which potentiate glucose-induced insulin secretion. Because of their insulinotropic action, their abnormal secretion may be involved in the pathogenesis of the hyperinsulinemia of childhood obesity. In this study, we used the hyperglycemic clamp with a small oral glucose load to assess the effect of childhood obesity on GIP response in seven prepubertal lean and 11 prepubertal obese children and in 14 lean adolescents and 10 obese adolescents. Plasma glucose was acutely raised to 11 mM by infusing i.v. glucose and kept at this concentration for 180 min. Each subject ingested oral glucose (30 g) at 120 min, and the glucose infusion was adjusted to maintain the plasma glucose plateau. Basal insulin and C-peptide concentrations and insulin secretion rates (calculated by the deconvolution method) were significantly greater in obese children compared with lean children (p < 0.001). Similarly, during the first 120 min of the clamp, insulin secretion rates were higher in obese than lean children. After oral glucose, plasma insulin, C-peptide, and insulin secretion rates further increased in all four groups. This incretin effect was 2-fold greater in obese versus lean adolescents (p < 0.001). Circulating plasma GIP concentrations were similar at baseline in all four groups and remained unchanged during the first 120 min of the clamp. After oral glucose, plasma GIP concentrations rose sharply in all groups (p < 0.002). Of note, the rise in GIP was similar in both lean and obese children. In conclusion, under conditions of stable hyperglycemia, the ingestion of a small amount of glucose elicited equivalent GIP responses in both lean and obese children. However, despite similar GIP responses, insulin secretion was markedly augmented in obese adolescents. Thus, in juvenile obesity, excessive alimentary beta-cell stimulation may be independent of the increased release of GIP.

Administration, Oral↗

PubMed1994

3D reconstruction by combining data from sections cut oblique to different unit cell axes.

Oblique section reconstruction (OSR) can produce a 3D image from a single micrograph of a section through a 2D or 3D crystal. Resolution, however, is limited in a direction perpendicular to the section plane. When data from sections cut at different orientations are combined, the inherent resolution limitation for single sections can be overcome. In the extreme, combination of sections cut oblique to different principal planes of the unit cell can produce a 3D reconstruction with isotropic resolution. The merging of data from different sections requires determination of section thickness and orientation. A method for section thickness determination is described that is generally applicable event to space groups with little or no symmetry. In addition, an approach has been developed to determine rotational orientation within the hexagonal lattice of insect flight muscle. Finally, an iterative least-squares fitting method is applied to determine a 3D set of deconvoluted structure factors from the merged data.

Adenylyl Imidodiphosphate↗

PubMed2000

Combinatorial libraries: a tool to design antimicrobial and antifungal peptide analogues having lytic specificities for structure-activity relationship studies.

In the race for supremacy, microbes are sprinting ahead. This warning by the World Health Organization clearly demonstrates that the spread of antibiotic-resistant bacteria leads to a global health problem and that antibiotics never seen before by bacteria are urgently needed. Antimicrobial peptides represent such a source for novel antibiotics due to their rapid lytic activity (within minutes) through disruption of cell membranes. However, due to the similarities between bacterial, fungal, and mammalian plasma cell membranes, a large number of antimicrobial peptides have low lytic specificities and exhibit a broad activity spectrum and/or significant toxic effect toward mammalian cells. Mutation strategies have allowed the development of analogues of existing antimicrobial peptides having greater lytic specificities, although such methods are lengthy and would be more efficient if the molecular mechanisms of action of antimicrobial peptides were clearly elucidated. Synthetic combinatorial library approaches have brought a new dimension to the design of novel biologically active compounds. Thus, a set of peptide analogues were generated based on the screening of a library built around an existing lytic peptide, and on a deconvolution strategy directed toward activity specificity. These peptide analogues also served as model systems to further study the effect of biomembrane mimetic systems on the peptides structural behavior relevant to their biological activities.

Amino Acid Sequence↗

PubMed1997

Evaluation of renographic and metabolic parameters in human kidney transplantation.

BACKGROUND: The aim of this work is to demonstrate that the value of the mean transit time (MTT) obtained from the 99mTc-MAG3 renogram deconvolution is related to the levels of adenine nucleotides determined in cortical biopsies from transplanted kidneys. METHODS: The functional state was estimated by means of the MTT and the initial height (H0) of the renal retention function obtained from the 99mTc-MAG3 renogram deconvolution and by the measure of adenine nucleotides obtained from biopsies. We studied 30 kidney graft recipients, 25 normal functioning grafts (NFG) and 5 with acute tubular necrosis (ATN). RESULTS: The MTT is significantly longer for ATN (p < 0.001). The initial uptake values (H0) are significantly lower for ATN (p < 0.001). The sum of adenine nucleotides (SAN) is significantly greater for NFG than for ATN (p < 0.001). The values of the MTT seem to reflect the energy state of the cells in transplanted kidney. CONCLUSION: The analysis of MTT may be indicative of the functional metabolic recovery and thus it may be predictive of the renal graft function at least in the same extent than the biochemical analysis of a cortical renal biopsy immediately after blood reperfusion of the tissue.

Adenine Nucleotides↗