bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutagenesis and Functional Characterization of the RNA and Protein Components of the
toxIN
Abortive Infection and Toxin-Antitoxin Locus of
Erwinia
Authors: Blower T. R. , Fineran P. C. , Johnson M. J. , Toth I. K. , Humphreys D. P. , Salmond G. P. C. 
Published: July 2009

ABSTRACT

Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multiple adaptive resistance mechanisms. These mechanisms include the abortive infection systems, which promote “altruistic suicide” of an infected cell, protecting the clonal population. A cryptic plasmid of
Erwinia carotovora
subsp.
atroseptica
, pECA1039, has been shown to encode an abortive infection system. This highly effective system is active across multiple genera of gram-negative bacteria and against a spectrum of phages. Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module. ToxIN is the first member of a new type III class of protein-RNA toxin-antitoxin modules, of which there are multiple homologues cross-genera. We characterized in more detail the abortive infection phenotype of ToxIN using a suite of
Erwinia
phages and performed mutagenesis of the ToxI and ToxN components. We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN. Furthermore, site-directed mutagenesis of ToxN revealed key conserved amino acids in this defining member of the new group of toxic proteins. The mechanism of phage activation of the ToxIN system was investigated and was shown to have no effect on the levels of the ToxN protein. Finally, evidence of negative autoregulation of the
toxIN
operon, a common feature of toxin-antitoxin systems, is presented. This work on the components of the ToxIN system suggests that there is very tight toxin regulation prior to suicide activation by incoming phage.
Processing and Stability of Inducibly ExpressedrpsOmRNA Derivatives inBacillus subtilis
Authors: Yao Shiyi , Bechhofer David H. 
Published: July 2009

ABSTRACTTheBacillus subtilis rpsOgene specifies a small (388-nucleotide), monocistronic mRNA that encodes ribosomal protein S15. We showed earlier thatrpsOmRNA decay intermediates accumulated to a high level in a strain lacking polynucleotide phosphorylase. Here, we used inducibly expressed derivatives ofrpsO, encoding smaller RNAs that had the complex 5′ region deleted, to study aspects of mRNA processing inB. subtilis. An IPTG (isopropyl-β-d-thiogalactopyranoside)-induciblerpsOtranscript that containedlacsequences at the 5′ end, calledlac-rpsORNA, was shown to undergo processing to result in an RNA that was 24 nucleotides shorter than full length. Such processing was dependent on the presence of an accessible 5′ terminus; alac-rpsORNA that contained a strong stem-loop at the 5′ end was not processed and was extremely stable. Interestingly, this stability depended also on ribosome binding to a nearby Shine-Dalgarno sequence but was independent of downstream translation. Either RNase J1 or RNase J2 was capable of processinglac-rpsORNA, demonstrating for the first time a particular in vivo processing event that could be catalyzed by both enzymes. Decay intermediates were detected in thepnpAstrain only for alac-rpsORNA that was untranslated. Analysis of processing of an untranslatedlac-rpsORNA in thepnpAstrain shortly after induction of transcription suggested that endonuclease cleavage at 3′-proximal sites was an early step in turnover of mRNA.
The Novel Genes
emmABC
Are Associated with Exopolysaccharide Production, Motility, Stress Adaptation, and Symbiosis in
Sinorhizobium meliloti
Authors: Morris Jennifer , González Juan E. 
Published: July 2009

ABSTRACT

The nitrogen-fixing symbiont
Sinorhizobium meliloti
senses and responds to constantly changing environmental conditions as it makes its way through the soil in search of its leguminous plant host,
Medicago sativa
(alfalfa). As a result, this bacterium regulates various aspects of its physiology in order to respond appropriately to stress, starvation, and competition. For example, exopolysaccharide production, which has been shown to play an important role in the ability of
S. meliloti
to successfully invade its host, also helps the bacterium withstand osmotic changes and other environmental stresses. In an effort to further elucidate the intricate regulation of this important cell component, we set out to identify genetic factors that may affect its production. Here we characterize novel genes that encode a small protein (EmmA) and a putative two-component system (EmmB-EmmC). A mutation in any of these genes leads to increased production of the symbiotically important exopolysaccharide succinoglycan. In addition,
emm
mutants display membrane-associated defects, are nonmotile, and are unable to form an optimal symbiosis with alfalfa, suggesting that these novel genes may play a greater role in the overall fitness of
S. meliloti
both during the free-living stage and in its association with its host.
Comparative Sequence Analysis ofMycobacterium lepraeand the New Leprosy-CausingMycobacterium lepromatosis
Authors: Han Xiang Y. , Sizer Kurt C. , Thompson Erika J. , Kabanja Juma , Li Jun , Hu Peter , Gómez-Valero Laura , Silva Francisco J. 
Published: July 2009

ABSTRACTMycobacterium lepromatosisis a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence fromMycobacterium leprae, a well-known cause of leprosy, that justifies the status ofM. lepromatosisas a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences withM. lepraesequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dSvalues) and nonsynonymous substitutions (dNvalues) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placedM. lepromatosisandM. lepraein a tight cluster with long terminal branches, implying that the divergence occurred long ago. ThedSanddNvalues were also much higher than those for other closest pairs of mycobacteria. ThedSvalues were 14 to 28% of thedSvalues forM. lepraeandMycobacterium tuberculosis, a more divergent pair of species. These results thus indicate thatM. lepromatosisandM. lepraediverged ∼10 million years ago. TheM. lepromatosispseudogenes analyzed that were also pseudogenes inM. lepraeshowed nearly neutral evolution, and their relative ages were similar to those ofM. lepraepseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate thatM. lepromatosisandM. lepraediverged from a common ancestor after the massive gene inactivation event described previously forM. leprae.
Cyclic di-GMP Allosterically Inhibits the CRP-Like Protein (Clp) of
Xanthomonas axonopodis
pv. citri
Authors: Leduc Jason L. , Roberts Gary P. 
Published: July 2009

ABSTRACT

The protein Clp from
Xanthomonas axonopodis
pv. citri regulates pathogenesis and is a member of the CRP (cyclic AMP receptor protein) superfamily. We show that unlike the DNA-binding activity of other members of this family, the DNA-binding activity of Clp is allosterically inhibited by its effector and that cyclic di-GMP serves as that effector at physiological concentrations.
Mutual Regulation of
ntcA
and
hetR
during Heterocyst Differentiation Requires Two Similar PP2C-Type Protein Phosphatases, PrpJ1 and PrpJ2, in
Anabaena
sp. Strain PCC 7120
Authors: Jang Jichan , Shi Lei , Tan Hui , Janicki Annick , Zhang Cheng-Cai 
Published: July 2009

ABSTRACT

The filamentous cyanobacterium
Anabaena
sp. strain PCC 7120 can form heterocysts for N
2
fixation. Initiation of heterocyst differentiation depends on mutual regulation of
ntcA
and
hetR
. Control of
hetR
expression by NtcA is partially mediated by
nrrA
, but other factors must be involved in this regulation.
Anabaena
has two closely related PP2C-type protein phosphatases, PrpJ1 (formerly PrpJ) and PrpJ2; PrpJ1 is involved in heterocyst maturation. In this study, we show that PrpJ2, like PrpJ1, has Mn
2+
-dependent phosphatase activity. We further demonstrate that whereas
prpJ2
is dispensable for cell growth under different nitrogen regimens tested, a double mutant with both
prpJ1
and
prpJ2
disrupted did not initiate heterocyst differentiation. Ectopic expression of
hetR
in the double mutant could rescue the failure to initiate heterocyst development, but the heterocysts formed, like those of a
prpJ1
single mutant, were not mature. The expression of
prpJ2
was enhanced during heterocyst development, and the upregulation of the gene was directly under the control of NtcA. Upregulation of both
ntcA
and
hetR
was affected in the double mutant. We propose that PrpJ1 and PrpJ2 together are required for mutual regulation of
ntcA
and
hetR
and are thus involved in regulation of the initiation of heterocyst differentiation.
Möbius voting for surface correspondence
Authors: Lipman Yaron , Funkhouser Thomas 
Published: July 2009

The goal of our work is to develop an efficient, automatic algorithm for discovering point correspondences between surfaces that are approximately and/or partially isometric.Our approach is based on three observations. First, isometries are a subset of the Möbius group, which has low-dimensionality -- six degrees of freedom for topological spheres, and three for topological discs. Second, computing the Möbius transformation that interpolates any three points can be computed in closed-form after a mid-edge flattening to the complex plane. Third, deviations from isometry can be modeled by a transportation-type distance between corresponding points in that plane.Motivated by these observations, we have developed a Möbius Voting algorithm that iteratively: 1) samples a triplet of three random points from each of two point sets, 2) uses the Möbius transformations defined by those triplets to map both point sets into a canonical coordinate frame on the complex plane, and 3) produces "votes" for predicted correspondences between the mutually closest points with magnitude representing their estimated deviation from isometry. The result of this process is a fuzzy correspondence matrix, which is converted to a permutation matrix with simple matrix operations and output as a discrete set of point correspondences with confidence values.The main advantage of this algorithm is that it can find intrinsic point correspondences in cases of extreme deformation. During experiments with a variety of data sets, we find that it is able to find dozens of point correspondences between different object types in different poses fully automatically.
Nurse Satisfaction Using Insulin Pens in Hospitalized Patients
Authors: Davis Estella M. , Bebee Anne , Crawford LeaAnne , Destache Chris 
Published: July 2009

Purpose The purpose of this study was to evaluate nurse satisfaction using pen devices compared with vials/syringes to administer insulin to hospitalized patients with diabetes. Methods A quasi-experimental 1-group posttest only study design was utilized to distribute a satisfaction survey to 54 registered nurses in a community hospital after implementation of insulin pen devices from July 2005 to May 2006 on 2 medical-surgical floors. Nurses completed a voluntary, anonymous, self-administered, postassessment, investigator-developed survey asking about the number of years practiced as a nurse and experience administering insulin to patients. The survey also asked about insulin administration satisfaction questions comparing insulin pen devices to vials/syringes, and estimated time to teach patients to self-inject insulin using either delivery method during the study period. Results In comparison to vials/syringes, the majority of nurses agreed that insulin pens were more convenient, simple and easy to use, and an overall improvement compared with conventional vials/syringes. There were no insulin-related needlestick injuries using the insulin pens and safety needles. Conclusion Nurses were satisfied with multiple aspects of insulin pens compared with vials/syringes. Implementation of insulin pen devices does not increase nursing time spent to teach patients to self-inject insulin and does not increase insulin-related needlestick injuries.
Correlation of Throwing Mechanics With Elbow Valgus Load in Adult Baseball Pitchers
Authors: Aguinaldo Arnel L. , Chambers Henry 
Published: July 2009

Background Studies have shown that various biomechanical factors affect valgus extension overload during baseball pitching; yet, their relationships are not clearly defined, and factors such as trunk rotation and arm slot have not been investigated. Hypothesis The onset of trunk rotation, with other biomechanical variables that define sequential body motion, will significantly predict elbow valgus loading. Study Design Descriptive laboratory study. Methods Sixty-nine adult baseball players pitched off an indoor mound during 3-dimensional motion analysis to measure whole body kinematics and kinetics at 240 Hz. Thirteen biomechanical variables were calculated and extracted for regression analysis to investigate their associations with elbow valgus load. A 2-way analysis of variance compared valgus torques between pitchers with 2 onsets of trunk rotation (before and after front-foot contact) and 2 arm slot positions (overhand and sidearm). Results Six biomechanical variables had significant correlations ( P < .02) with elbow valgus torque—with maximum shoulder external rotation, elbow flexion at peak valgus torque, and elbow valgus loading rate accounting for 68% of its variance. Reduced elbow valgus torques were associated with increased elbow flexion ( P < .01). Players who initiated trunk rotation before front-foot contact had significantly higher elbow valgus torques than did those who rotated afterward ( P = .02). Fourteen pitchers displayed a sidearm delivery and had significantly higher elbow valgus torques than did those with an overhand arm slot position. Conclusion Valgus torque at the elbow during baseball pitching is associated with 6 biomechanical variables of sequential body motion. A condition of late trunk rotation, reduced shoulder external rotation, and increased elbow flexion appeared to be most closely related to valgus torque. Sidearm pitchers appeared to be more susceptible than overhand pitchers to reduced elbow valgus torque. Clinical Relevance The biomechanical findings of this study offer scientific feedback for developing methods used to minimize the effects of valgus load on pitching-related elbow injuries.
Assessment of Differences Between the Modified Cincinnati and International Knee Documentation Committee Patient Outcome Scores
Authors: Agel Julie , LaPrade Robert F. 
Published: July 2009

Background Functional outcome questionnaires have become a common part of patient follow-up in the orthopaedic community. The modified Cincinnati Knee Rating System and the International Knee Documentation Committee (IKDC) subjective scale were designed to provide clinicians with information regarding a patient’s functional and clinical status after knee surgery. Hypothesis The functional outcome data reported on the modified Cincinnati Knee Rating System and the IKDC subjective questionnaire are equivalent. Study Design Cohort study (diagnosis); Level of evidence, 2. Methods Between 2000 and 2007, all patients with complex knee disorders seen in our orthopaedic clinic were prospectively followed and given simultaneously the modified Cincinnati Knee Rating System and the IKDC subjective questionnaires to report their functional outcomes. The total scores of each instrument were compared at each time of evaluation. As a measure of responsiveness, the standardized response means were calculated. A second within-patient analysis was also performed to determine if the results would be different when looked at by the patient. Results There were a total of 130 patients with a total of 444 modified Cincinnati Knee Rating System questionnaires and 462 IKDC subjective complete questionnaires included in the study. Overall total scores on both the modified Cincinnati Knee Rating System and the IKDC subjective questionnaires were equivalent in a population analysis. Overall total scores showed improvement in function over time from preoperative measurement through the 2-year follow-up. The individual patient analysis demonstrated that, for a specific patient, it was possible that up to 34% of the population would report a total score of more than 10 points difference, depending on the scale selected. Conclusion The modified Cincinnati Knee Rating System and the IKDC subjective rating questionnaires reported by patient population provide similar results. The practitioner who is not performing a population-based study but following individual patients for recovery will find that the individual questionnaires may offer different functional limitations. Individual differences were lost in the population means, with the approximate balance of positive and negative score differences masking the individual patient differences.
Injury Patterns in Division I Collegiate Swimming
Authors: Wolf Brian R. , Ebinger Alexander E. , Lawler Michael P. , Britton Carla L. 
Published: July 2009

Background In the last 25 years, it is estimated that over 42,000 male and female swimmers have competed at the National Collegiate Athletic Association (NCAA) Division I-A level. Despite the magnitude of these numbers, little is known about the epidemiology of collegiate swimming injuries. Purpose To describe the pattern of injuries incurred for one NCAA Division I collegiate men’s and women’s swimming team over 5 seasons. Study Design Descriptive epidemiology study. Methods Musculoskeletal and head injuries reported in the Sports Injury Management System for a Division I swimming team from 2002–2007 were identified. Gender, body part, year of eligibility, position, stroke specialty, scholarship status, and team activity during which the injury occurred and lost time were recorded. Risk of injury was assessed relative to gender, stroke specialty, and year of eligibility. Results From 2002–2007, 44 male and 50 female athletes competed for the University of Iowa swimming and diving team. The overall injury rates were estimated as 4.00 injuries per 1000 exposures for men and 3.78 injuries per 1000 exposures for women. Thirty-seven percent of injuries resulted in missed time. The shoulder/upper arm was the most frequently injured body part followed by the neck/back. Freshman swimmers suffered the most injuries as well as the highest mean number of injuries per swimmer. A significant pattern of fewer injuries in later years of eligibility was also demonstrated. The relative risk (RR) for injury was higher among nonfreestyle stroke specialties (RR, 1.33 [1.00–1.77]). Injury most often occurred as a result of, or during, practice for all swimmers. However, 38% of injuries were the result of team activities outside of practice or competition, such as strength training. No significant relationship was found between occurrence of injury and gender or scholarship status. There was no significant relationship between body part injured and stroke specialty. An increased number of total injuries and an increased risk of injuries in freshman collegiate swimmers were found. Conclusion Particular attention should be given to swimmers making the transition into collegiate level swimming. These data also suggest that injury surveillance and potential prevention strategies should focus on the shoulder for in-pool activities and the axial spine for cross-training activities.
The Effect of Pitching Biomechanics on the Upper Extremity in Youth and Adolescent Baseball Pitchers
Authors: Davis J.T. , Limpisvasti Orr , Fluhme Derrick , Mohr Karen J. , Yocum Lewis A. , ElAttrache Neal S. , Jobe Frank W. 
Published: July 2009

Background Increased pitch counts have been linked to increased complaints of shoulder and elbow pain in youth baseball pitchers. Improper pitching mechanics have not been shown to adversely affect the upper extremity in youth pitchers. Hypothesis The correct performance of 5 biomechanical pitching parameters correlates with lower humeral internal rotation torque and elbow valgus load, as well as higher pitching efficiency, in youth and adolescent pitchers. Study Design Descriptive laboratory study. Methods In sum, 169 baseball pitchers (aged 9-18) were analyzed using a quantitative motion analysis system and a high-speed video while throwing fastballs. The correct performance of 5 common pitching parameters was compared with each pitcher's age, humeral internal rotation torque, elbow valgus load, and calculated pitching efficiency. Results Motion analysis correlated with video analysis for all 5 parameters (P <. 05). Youth pitchers (aged 9-13) performing 3 or more parameters correctly showed lower humeral internal rotation torque, lower elbow valgus load, and higher pitching efficiency (P <. 05). Conclusions Youth pitchers with better pitching mechanics generate lower humeral internal rotation torque, lower elbow valgus load, and more efficiency than do those with improper mechanics. Proper pitching mechanics may help prevent shoulder and elbow injuries in youth pitchers. Clinical Relevance The parameters described in this study may be used to improve the pitching mechanics of youth pitchers and possibly reduce shoulder and elbow pain in youth baseball pitchers.
Architecture of the Counter Insurgency Experiment
Authors: Monday Paul 
Published: July 2009

The Counter Insurgency (COIN) Experiment was performed in March 2007 using a distributed network. It focused on simulating urban operations in Central Asia in 2015. A major goal of the experiment was to demonstrate the use of a complex Models and Simulation federation to train and evaluate doctrine for a COIN Environment. Participating federates included OFOTB, FireSim, JSAF, CultureSim, EADSim, CMS2, UC, ACRT, ACRT-DR, JNEM, ISM, SA Server, MC2, Communications & Electronics Research Development & Engineering Center (CERDEC), CES, AOI Server, EFS, Reporter, DataLogger and SEAMS.This was an entity-level distributed simulation event that included sites at Ft Knox, Ft Sill, Ft Bliss, and Huntsville, using the Distributed Interactive Simulation (DIS) and HLA protocols.Approximate entity counts included 1000 US vehicles and soldiers, 1000 Local Police and Army, 1200 insurgents, and 20,000 civilians from various population groups. Several new and enhanced models contributed to the richness of the COIN environment. A Force model was developed that allowed each station to control its rules of engagement, which is crucial for a situation where the enemy depend on who and where you are. A model of uniformed entities versus plain clothes was added since insurgents do not generally show themselves as such.The JNEM/ISM provided real-time feedback on the mood of the various civilian population groups. A new model of Improvised Explosive Devices (IEDs) was developed that simulated several trigger types, decoys and countermeasures. Suppressive effects were added, including non-lethal rounds. The area-of-interest model was improved to allow good simulation performance in a dense urban environment. The terrain database had 10,000 fully modeled multi-elevation buildings along with 650,000 volume buildings. COIN marked a dramatic leap forward in our ability to simulate urban warfare. It showed that it is possible to use entity-level simulation to examine situations relevant to today’s Army, such as stability operations, counter insurgencies, and the hybrid enemy.This experiment demonstrated many first uses of innovative models and techniques that are now standard, and established a benchmark of success in terms of its fidelity, performance, and complexity.