bluuebunny/crossref_metadata_2025_split huggingface dataset:
Error compensation for fused deposition modeling (FDM) machine by correcting slice files
Authors: Tong Kun , Joshi Sanjay , Amine Lehtihet E. 
Published: January 2008

PurposeThe purpose of this research is to extend the previous approach to software error compensation to fused deposition modeling (FDM) machines and explores the approach to apply compensation by correcting slice files.Design/methodology/approachIn addition to applying the stereolithography (STL) file‐based compensation method from earlier research; a new approach using the slice file format to apply compensation is presented. Under this approach, the confounded effects of all errors in a FDM machine are mapped into a “virtual” parametric machine error model. A 3D artifact is built on the FDM machine and differences between its actual and nominal dimensions are used to estimate the coefficients of the error functions. A slice file compensation method is developed and tested on two types of parts as a means for further improving the error compensation for feature form error improvement. STL file compensation is also applied to a specific FDM 3000 machine and the results are compared with those of a specific SLA 250 machine.FindingsThe two compensation methods are compared. Although, the slice file compensation method theoretically allows higher compensation resolution, the actual machine control resolution of the FDM machine can be a limitation which makes the difference between STL compensation and slice file compensation indistinguishable. However, as the control resolution is increased, this method will make it possible to provide a higher degree of compensation.Originality/valueCompensation method applied to slice file format is developed for FDM machines and its limitations are explored. Based on the experimental study, dimensional accuracy of parts is considerably improved by the software error compensation approach.
Achieving transformative sustainability learning: engaging head, hands and heart
Authors: Sipos Yona , Battisti Bryce , Grimm Kurt 
Published: January 2008

PurposeThe current UN Decade of Education for Sustainable Development echoes many scholars' calls to re‐envision education for sustainability. Short of a complete overhaul of education, the paper seeks to propose learning objectives that can be integrated across existing curricula. These learning objectives are organized by head, hands and heart – balancing cognitive, psychomotor and affective domains. University programs and courses meeting these learning objectives exhibit an emergent property here termed transformative sustainability learning (TSL).Design/methodology/approachTheoretically, TSL grew from traditions of sustainability education and transformative education. Practically, TSL emerged from experimental learning collaborations sponsored by the University of British Columbia in 2003 and 2004 in an effort to enable explicit transitions to sustainability‐oriented higher education. Primarily through action research, these community‐based, applied learning experiences constituted cyclical processes of innovation, implementation and reflection.FindingsThe paper finds: advancement of head, hands and heart as an organizing principle by which to integrate transdisciplinary study (head); practical skill sharing and development (hands); and translation of passion and values into behaviour (heart); development of a cognitive landscape for understanding TSL as a unifying framework amongst related sustainability and transformative pedagogies that are inter/transdisciplinary, practical and/or place‐based; creation of learning objectives, organized to evaluate a course or program's embodiment of TSL.Originality/valueBy enabling change within existing structures of higher education, the paper complements and contributes to more radical departures from the institution. The work to date demonstrates potential in applying this learning framework to courses and programs in higher education.
Interchange of autoinhibitory domain conformations in plasma‐membrane Ca2+‐ATPase–calmodulin complexes
Authors: Mandal Abhijit , Liyanage Mangala Roshan , Zaidi Asma , Johnson Carey K. 
Published: January 2008

AbstractThe Ca2+ signaling protein calmodulin (CaM) stimulates Ca2+ pumping in the plasma‐membrane Ca2+‐ATPase (PMCA) by binding to an autoinhibitory domain, which then dissociates from the catalytic domain of PMCA to allow full activation of the enzyme. We measured single‐molecule fluorescence trajectories with polarization modulation to track the conformation of the autoinhibitory domain of PMCA pump bound to fluorescently labeled CaM. Interchange of the autoinhibitory domain between associated and dissociated conformations was detected at a physiological Ca2+ concentration of 0.15 μM, where the enzyme is only partially active, but not at 25 μM, where the enzyme is fully activated. In previous work we showed that the conformation of the autoinhibitory domain in PMCA–CaM complexes could be monitored by the extent of modulation of single‐molecule fluorescence generated with rotating excitation polarization. In the present work, we determined the timescale of association and dissociation of the autoinhibitory domain with the catalytic regions of the PMCA. Association of the autoinhibitory domain was rare at a high Ca2+ concentration (25 μM). At a lower Ca2+ concentration (0.15 μM), conformations of the autoinhibitory domain interchanged with a dissociation rate of 0.042 ± 0.011 sec−1 and an association rate of 0.023 ± 0.006 sec−1. The results indicate that the response time of PMCA upon a reduction in Ca2+ is limited to tens of seconds by autoinhibitory dynamics. This property may reduce the sensitivity of PMCA to transient reductions in intracellular Ca2+. We suggest that the dynamics of the autoinhibitory domain may play a novel role in regulating PMCA activity.
Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site
Authors: Mochalkin Igor , Lightle Sandra , Narasimhan Lakshmi , Bornemeier Dirk , Melnick Michael , VanderRoest Steven , McDowell Laura 
Published: January 2008

AbstractN‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram‐negative and Gram‐positive bacteria. Here we disclose a 1.9 Å resolution crystal structure of a synthetic small‐molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high‐throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC50 ∼ 18 μM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc‐1‐P substrate‐binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure‐guided design of a new class of mechanism‐based inhibitors of GlmU.
Efficient point mutagenesis in mycobacteria using single‐stranded DNA recombineering: characterization of antimycobacterial drug targets
Authors: Van Kessel Julia C. , Hatfull Graham F. 
Published: January 2008

SummaryConstruction of genetically isogenic strains of mycobacteria is complicated by poor recombination rates and the lack of generalized transducing phages for Mycobacterium tuberculosis. We report here a powerful method for introducing single point mutations into mycobacterial genomes using oligonucleotide‐derived single‐stranded DNA recombineering and mycobacteriophage‐encoded proteins. Phage Che9c gp61‐mediated recombination is sufficiently efficient that single base changes can be introduced without requirement for direct selection, with isogenic mutant strains identified simply by PCR. Efficient recombination requires only short (50 nucleotide) oligonucleotides, but there is an unusually strong strand bias and an oligonucleotide targeting lagging strand DNA synthesis can recombine more than 10 000‐fold efficiently than its complementary oligonucleotide. This ssDNA recombineering provides a simple assay for comparing the activities of related phage recombinases, and we find that both Escherichia coli RecET and phage λ Red recombination proteins function inefficiently in mycobacteria, illustrating the utility of developing recombineering in new bacterial systems using host‐specific bacteriophage recombinases. ssDNA mycobacterial recombineering provides a simple approach to characterizing antimycobacterial drug targets, and we have constructed and characterized single point mutations that confer resistance to isoniazid, rifampicin, ofloxacin and streptomycin.
XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose synthesis and programmed cell death in xylem
Authors: Zhao Chengsong , Avci Utku , Grant Emily H. , Haigler Candace H. , Beers Eric P. 
Published: January 2008

SummaryMembers of the large Arabidopsis NAC domain transcription factor family are regulators of meristem development, organ elongation and separation, and deposition of patterned secondary cell walls. XYLEM NAC DOMAIN 1 (XND1) is highly expressed in xylem. Changes observed for XND1 knockout plants compared with wild‐type Arabidopsis thaliana included a reduction in both plant height and tracheary element length and an increase in metaxylem relative to protoxylem in roots of plants treated with the proteasome inhibitor MG132. Overexpression of XND1 resulted in extreme dwarfism associated with the absence of xylem vessels and little or no expression of tracheary element marker genes. In contrast, phloem marker‐gene expression was not altered and phloem‐type cells still formed. Transmission electron microscopy showed that parenchyma‐like cells in the incipient xylem zone in hypocotyls of XND1 overexpressors lacked secondary wall thickenings and retained their cytoplasmic content. Considered together, these findings suggest that XND1 affects tracheary element growth through regulation of secondary wall synthesis and programmed cell death.
Developmental information but not promoter activity controls the methylation state of histone H3 lysine 4 on two photosynthetic genes in maize
Authors: Danker Tanja , Dreesen Björn , Offermann Sascha , Horst Ina , Peterhänsel Christoph 
Published: January 2008

SummaryWe have investigated the establishment of histone H3 methylation with respect to environmental and developmental signals for two key genes associated with C4 photosynthesis in maize. Tri‐methylation of histone H3 lysine 4 (H3K4) in roots and leaves was shown to be controlled by autonomous cell‐type‐specific developmental signals that are independent of illumination and therefore independent of the initiation of transcription. Di‐ and mono‐methylation of H3K4 act antagonistically to this process. The modifications were already established in etiolated seedlings, and remained stable when genes were inactivated by dark treatment or pharmaceutical inhibition of transcription. Constitutive di‐methylation of H3K9 was concomitantly detected at specific gene positions. The data support a histone code model whereby cell‐type‐specific signals induce the formation of a chromatin structure that potentiates gene activation by environmental cues.
Biosynthesis of circular proteins in plants
Authors: Gillon Amanda D. , Saska Ivana , Jennings Cameron V. , Guarino Rosemary F. , Craik David J. , Anderson Marilyn A. 
Published: January 2008

SummaryPlant cyclotides are a large family of naturally occurring circular proteins that are produced from linear precursors containing one, two or three cyclotide domains. The mechanism of excision of the cyclotide domains and ligation of the free N‐ and C‐termini to produce the circular peptides has not been elucidated. Here, we investigate production of the prototypic cyclotide kalata B1 from the precursor Oak1 from the African plant Oldenlandia affinis. Immunoprecipitation experiments and MALDI‐TOF mass spectrometry analysis showed that O. affinis only produces mature kalata B1, whereas transgenic Arabidopsis thaliana, Nicotiana tabacum and Nicotiana benthamiana produced both linear and circular forms. Circular peptides were not produced when a highly conserved asparagine residue at the C‐terminal processing site of the cyclotide domain was replaced with an alanine or an aspartate residue, or when the conserved C‐terminal tripeptide motif was truncated. We propose that there are two processing pathways in planta: one to produce the mature cyclotide and the other to produce linear variants that ultimately cannot be cyclized.
Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis
Authors: March‐Díaz Rosana , García‐Domínguez Mario , Lozano‐Juste Jorge , León José , Florencio Francisco J. , Reyes José C. 
Published: January 2008

SummaryOne of the mechanisms involved in chromatin remodelling is so‐called ‘histone replacement’. An example of such a mechanism is the substitution of canonical H2A histone by the histone variant H2A.Z. The ATP‐dependent chromatin remodelling complex SWR1 is responsible for this action in yeast. We have previously proposed the existence of an SWR1‐like complex in Arabidopsis by demonstrating genetic and physical interaction of the components SEF, ARP6 and PIE1, which are homologues of the yeast Swc6 and Arp6 proteins and the core ATPase Swr1, respectively. Here we show that histone variant H2A.Z, but not canonical H2A histone, interacts with PIE1. Plants mutated at loci HTA9 and HTA11 (two of the three Arabidopsis H2A.Z‐coding genes) displayed developmental abnormalities similar to those found in pie1, sef and arp6 plants, exemplified by an early‐flowering phenotype. Comparison of gene expression profiles revealed that 65% of the genes differentially regulated in hta9 hta11 plants were also mis‐regulated in pie1 plants. Detailed examination of the expression data indicated that the majority of mis‐regulated genes were related to salicylic acid‐dependent immunity. RT‐PCR and immunoblotting experiments confirmed constitutive expression of systemic acquired resistance (SAR) marker genes in pie1, hta9 hta11 and sef plants. Variations observed at the molecular level resulted in phenotypic alterations such as spontaneous cell death and enhanced resistance to the phytopathogenic bacteria Pseudomonas syringae pv. tomato. Thus, our results support the existence in Arabidopsis of an SWR1‐like chromatin remodelling complex that is functionally related to that described in yeast and human, and attribute to this complex a role in maintaining a repressive state of the SAR response.
No Change Detected in Body Weight, Scrotal Circumference, Semen Characteristics and Sexual Behaviour during the Development of Prepubertal Milchschaf Lambs after Weekly Administration of eCG
Authors: Ungerfeld R , Bielli A 
Published: January 2008

ContentsTo study the effects of equine chorionic gonadotropin (eCG) on pubertal development, 38 Milchschaf spring born male lambs fathered by the same ram and grazing over native pasture as a single mob during all the experiment were divided into three groups as follows: group 100 (100 IU of eCG weekly i.m., n = 11), group 400 (400 IU of eCG weekly i.m., n = 12) and group 0 (controls, n = 15). Lambs were weighed and scrotal circumference was registered every 2 weeks since birth until 170 days of age (end of experiment). On days 125 and 167 semen was collected using an electroejaculator. Semen volume and concentration, mass and individual sperm motility (scale 0 to 5) and total number of spermatozoa in the ejaculate were recorded. The sexual behaviour of the lambs was evaluated twice, on days 127 and 170 in a pen test with oestrous ewes. There were no significant effects of treatment on body weight or scrotal circumference, semen characteristics or sexual behaviour. At least in the administration regimens tested, eCG treatment has no effect on prepubertal reproductive development of male lambs.
Comparison of hand‐assisted laparoscopic and open donor nephrectomy in living donors
Authors: Minnee Robert C , Bemelman Frederike , Kox Cees , Surachno Susanto , ten Berge Ineke JM , Bemelman Willem A , Idu Mirza M 
Published: January 2008

Objectives:  Although the advent of (hand‐assisted) laparoscopic donor nephrectomy has had a positive effect on the donor pool, there is still some concern about the increased morbidity and safety of the laparoscopic donor nephrectomy. The aim of this study was to compare the results of hand‐assisted laparoscopic donor nephrectomy (HALD) with open donor nephrectomy (ODN).Methods:  A single‐center non‐randomized analysis of 202 living donor kidney transplantations (44 ODN, 158 HALD) between January 1995 and April 2006 was conducted.Results:  The left kidney was harvested in 75% in the ODN group and 53% in the HALD group (P = 0.009). There was no conversion in the HALD group. Mean donor operative time for HALD (174 min) was longer than for ODN (124 min, P < 0.001). The mean donor hospital stay (4.9 days vs 9.6 days, P < 0.001) was significantly less for HALD. HALD had lower mean creatinine values at day 7 and 1 month (P = 0.001 and P = 0.002) and lower urological complication rates (P = 0.02) compared with ODN. The 1‐year graft survival rates of the ODN and the HALD group were 84% and 95% (P = 0.006), respectively.Conclusion:  hand‐assisted laparoscopic donor nephrectomy is a safe procedure for a donor nephrectomy with potential benefits compared with ODN.
The GacA global regulator is required for the appropriate expression of Erwinia chrysanthemi 3937 pathogenicity genes during plant infection
Authors: Lebeau Aurore , Reverchon Sylvie , Gaubert Stéphane , Kraepiel Yvan , Simond‐Côte Elizabeth , Nasser William , Van Gijsegem Frédérique 
Published: January 2008

SummaryPathogenicity of the phytopathogenic enterobacterium Erwinia chrysanthemi, the causal agent of soft rot disease on many plants, is a complex process involving several factors whose production is regulated by a complex, intertwined regulatory network. In this work we characterized the GacA regulator, member of the GacS–GacA two‐component system, as a global regulator which is required for disease expression but not for bacterial multiplication in planta during the first stages of the plant infection. GacA was shown to control the expression of plant cell wall‐degrading enzymes and hrp genes in vitro. Analysis of virulence gene expression during infection of Arabidopsis thaliana revealed a coordinated expression of these virulence genes at 12 h post infection and showed that GacA is required for the appropriate production of virulence factors in planta. GacA might partly act by negatively controlling the expression of the pecT gene encoding the global repressor PecT, indicating a hierarchy in the pathways involved in the E. chrysanthemi regulatory network.
A metagenomic analysis of soil bacteria extends the diversity of quorum‐quenching lactonases
Authors: Riaz Kashif , Elmerich Claudine , Moreira David , Raffoux Aurélie , Dessaux Yves , Faure Denis 
Published: January 2008

SummaryA metagenomic library of 10 121 clones, generated from bacteria inhabiting a pasture soil from France, was screened for the presence of fosmids conferring either N‐acylhomoserine lactone (NAHL) synthesis or NAHL degradation ability upon their Escherichia coli host. No clone producing NAHLs was identified whereas one, containing a 31 972 bp insert in fosmid p2H8, allowed NAHL degradation. This led to the cloning and identification of a gene, qlcA, encoding an NAHL‐lactonase activity, as judged by lactone‐ring closure and HPLC/MS analyses of NAHL degradation products. The qlcA gene efficiently quenched quorum‐sensing regulated pathogenic functions when expressed in Pectobacterium carotovorum. The QlcA peptide belongs to the family of zinc‐dependent metallohydrolases and appears to be distantly related to other NAHL‐lactonases discovered in Agrobacterium, Bacillus, Photorhabdus and Rhizobium. In‐silico analysis of the metagenomic insert revealed the occurrence of 20 orf, with a constant GC% and codon usage, suggesting a unique bacterial origin. Nine out of these 20 orf were homologous to genes encoding biosynthesis of arginine; they were clustered with an unusual succession argFJADBCRGH. The fosmid p2H8 is able to complement the argA, argB and argC mutants in E. coli. Phylogenetic analysis showed that 9 orf out of 20 were related to sequences from members of the Acidobacteria, supporting the hypothesis that the analysed insert might be originated from an organism related to this phylum.
Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil
Authors: Nicolaisen Mette Haubjerg , Bælum Jacob , Jacobsen Carsten Suhr , Sørensen Jan 
Published: January 2008

SummaryA modified protocol for simultaneous extraction of RNA and DNA, followed by real‐time polymerase chain reaction quantification, was used to investigate tfdA gene expression during in situ degradation of the herbicide MCPA (4‐chloro‐2‐methylphenoxy‐acetic acid) in soil. tfdA encodes an α‐ketoglutarate‐dependent dioxygenase catalysing the first step in the degradation pathway of MCPA and 2,4‐D (2,4‐dichlorophenoxy‐acetic acid). A linear recovery of tfdA mRNA over three orders of magnitude was shown, and the tfdA mRNA level was normalized using the tfdA mRNA/DNA ratio. The density of active cells required for tfdA mRNA detection was 105 cells g−1 soil. Natural soil microcosms inoculated with Cupriavidus necator (formerly Ralstonia eutropha) AEO106 (pRO101) cells were amended with four different MCPA concentrations (2, 20, 50 and 150 mg kg−1). Mineralization rates were estimated by quantification of 14CO2 emission from degradation of 14C‐MCPA. tfdA mRNA was detected 1 h after amendment at all four concentrations. In soils amended with 2 and 20 mg kg−1, the mRNA/DNA ratio for tfdA demonstrated a sharp transient maximum of tfdA expression from no to full expression within 3 and 6 h respectively, followed by a decline and complete loss of expression after 19 and 43 h. A more complex pattern of tfdA expression was observed for the higher 50 and 150 mg kg−1 amendments; this coincided with growth of C. necator AEO106 (pRO101) in the system. Repeated amendment with MCPA after 2 weeks in the 20 mg kg−1 scenario revealed a sharp increase of tfdA mRNA, and absence of a mineralization lag phase. For all amendments, tfdA mRNA was detectable only during active mineralization, and thus revealed a direct correlation between tfdA mRNA presence and microbial degrader activity. The present study demonstrates that direct analysis of functional gene expression dynamics by quantification of mRNA can indeed be made in natural soil.