bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome of the Extremely Radiation-Resistant Bacterium
Deinococcus radiodurans
Viewed from the Perspective of Comparative Genomics
Authors: Makarova Kira S. , Aravind L. , Wolf Yuri I. , Tatusov Roman L. , Minton Kenneth W. , Koonin Eugene V. , Daly Michael J. 
Published: January 2003

SUMMARY
The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.
Cytokinesis in Prokaryotes and Eukaryotes: Common Principles and Different Solutions
Authors: Nanninga Nanne 
Published: January 2003

SUMMARYCytokinesis requires duplication of cellular structures followed by bipolarization of the predivisional cell. As a common principle, this applies to prokaryotes as well as eukaryotes. With respect to eukaryotes, the discussion has focused mainly on Saccharomyces cerevisiae and on Schizosaccharomyces pombe. Escherichia coli and to a lesser extent Bacillus subtilis have been used as prokaryotic examples. To establish a bipolar cell, duplication of a eukaryotic origin of DNA replication as well as its genome is not sufficient. Duplication of the microtubule-organizing center is required as a prelude to mitosis, and it is here that the dynamic cytoskeleton with all its associated proteins comes to the fore. In prokaryotes, a cytoskeleton that pervades the cytoplasm appears to be absent. DNA replication and the concomitant DNA segregation seem to occur without help from extensive cytosolic supramacromolecular assemblies but with help from the elongating cellular envelope. Prokaryotic cytokinesis proceeds through a contracting ring, which has a roughly 100-fold-smaller circumference than its eukaryotic counterpart. Although the ring contains proteins that can be considered as predecessors of actin, tubulin, and microtubule-associated proteins, its macromolecular composition is essentially different.
Cytoskeleton of Apicomplexan Parasites
Authors: Morrissette Naomi S. , Sibley L. David 
Published: January 2003

SUMMARYThe Apicomplexa are a phylum of diverse obligate intracellular parasites including Plasmodium spp., the cause of malaria; Toxoplasma gondii and Cryptosporidium parvum, opportunistic pathogens of immunocompromised individuals; and Eimeria spp. and Theileria spp., parasites of considerable agricultural importance. These protozoan parasites share distinctive morphological features, cytoskeletal organization, and modes of replication, motility, and invasion. This review summarizes our current understanding of the cytoskeletal elements, the properties of cytoskeletal proteins, and the role of the cytoskeleton in polarity, motility, invasion, and replication. We discuss the unusual properties of actin and myosin in the Apicomplexa, the highly stereotyped microtubule populations in apicomplexans, and a network of recently discovered novel intermediate filament-like elements in these parasites.
A Randomized, Controlled Double‐blind Trial of Usual‐dose versus High‐dose Albuterol via Continuous Nebulization in Patients with Acute Bronchospasm
Authors: Stein John , Levitt M. Andrew 
Published: January 2003

Abstract Objective: Continuous nebulization is becoming more popular in the management of acute bronchospasm in the emergency department (ED). Controversy still exists as to the optimal dose of albuterol for such exacerbations. The present study hypothesis was that there is no difference between continuous nebulization of albuterol at 7.5 mg/hr (usual dose) and 15 mg/hr (high dose) in peak flow improvement up to three hours. Methods: This was a randomized, controlled, double‐blind trial, set in an urban county teaching ED. One hundred twenty‐seven patients with acute bronchospasm and an initial peak flow (PF) less than 75% predicted were enrolled. Patients were randomized to usual‐dose (UD) or high‐dose (HD) groups along with a standard treatment protocol. Primary end‐points were analyzed using repeated‐measures analysis of variance (ANOVA), and 95% confidence intervals (95% CIs) are given for such variables. Results: Sixty‐seven patients were randomized to the HD albuterol group, and 63 completed the study. Sixty patients were randomized to the UD group, and 55 completed the study. Repeated‐measures ANOVA found no difference in systolic blood pressure, diastolic blood pressure, pulse, respiratory rate, Borg dyspnea scale score, and peak flow over time between the groups. The mean (±SD) peak flow improvement at one hour was UD 51 (±49) L/min vs. HD 45 (±50) L/min, mean difference 6.8 L/min (95% CI = ‐11 to 24.9 L/min). Adjusting for baseline, the percentage increase in peak flow at one hour was UD 44% (±60%) vs. HD 30% (±40%), mean difference 14% (95% CI = ‐4.4% to 32.4%). Time to disposition showed a mean of 188 (±129) minutes for UD and 230 (±183) minutes for HD, mean difference 42 minutes (95% CI = ‐170 to 101 min). One patient in the HD group was intubated. Admission rate was UD 70.9% vs. HD 65%, mean difference 5.9% (95% CI = ‐10.9% to 22.7%). Conclusions: In treating acute, moderately‐severe bronchospastic ED patients with peak flow less than 75% of predicted with albuterol by continuous nebulization, 15 mg/hr appears to offer no advantage over 7.5 mg/hr in peak flow improvement or length of stay in the ED.
Predictors of Emergency Medical Services Utilization by Elders
Authors: Shah Manish N. , Glushak Cai , Karrison Theodore G. , Mulliken Robert , Walter James , Friedmann Peter D. , Hayley Deon Cox , Chin Marshall H. 
Published: January 2003

Abstract Objective: Elders (age ≥ 65 years) frequently use emergency medical services (EMS) for care. Understanding reasons for EMS use by elders may allow better management of EMS demand. To the best of the authors' knowledge, no studies have identified patient characteristics associated with EMS use by elders. This study aimed to identify patient attributes associated with elder EMS users. Methods: This was a prospective cohort study of non‐institutionalized elders presenting to an urban university hospital emergency department. Nine hundred thirty elder patients completed the survey. The authors asked patients about access to care, health beliefs, and reasons for requesting EMS assistance. Univariate and logistic regression were used to identify predictors of EMS use. Results: The sample had a mean age of 76 years; 37% were male; 79% were African American. Thirty percent arrived via EMS. Sixty‐five percent of those transported and 46% of those not transported by EMS were admitted to the hospital (p < 0.001). Reported reasons for using EMS transport included immobility (33%), illness (22%), request by others (21%), instruction from health care providers (10%), and lack of transportation (10%). Logistic regression identified symptom onset within four hours of seeking care (OR = 3.1), age ≥ 85 years (OR = 1.63), increased deficiencies in activities of daily living (OR = 1.40 per deficiency), worse physical functioning (OR = 1.14/10 points), and worse social functioning (OR = 1.06/10 points) as factors associated with EMS use. Conclusions: Elders report using EMS because of immobility, perceived medical needs, or requests by others. Similarly, the presence of acute illness symptoms, older age, and poor social and physical function, rather than health beliefs, predict EMS use among elders. These factors must be considered when managing the demand for EMS services.
Patient Safety: A Curriculum for Teaching Patient Safety in Emergency Medicine
Authors: Cosby Karen S. , Croskerry Pat 
Published: January 2003

AbstractThe last decade has witnessed a growing awareness of medical error and the inadequacies of our health care delivery systems. The Harvard Practice Study and subsequent Institute of Medicine Reports brought national attention to long‐overlooked problems with health care quality and patient safety. The Committee on Quality of Health Care in America challenged professional societies to develop curriculums on patient safety and adopt patient safety teaching into their training and certification requirements. The Patient Safety Task Force of the Society for Academic Emergency Medicine (SAEM) was charged with that mission. The curriculum presented here offers an approach to teaching patient safety in emergency medicine.
Emergency Department Services for Patients with Alcohol Problems: Research Directions
Authors: Hungerford Daniel W. , Pollock Daniel A. 
Published: January 2003

AbstractThis report summarizes recommendations on research directions developed from the conference “Alcohol Problems among Emergency Department Patients: Research on Identification and Intervention.” The conference was developed in order to evaluate the existing state of the art research on emergency department interventions for alcohol problems, and offer further recommendations for research.
Emergency Bedside Ultrasound to Detect Pneumothorax
Authors: Chan Stewart Siu Wa 
Published: January 2003

AbstractA relatively new application of emergency ultrasound is its use in the diagnosis of pneumothorax. In patients with major trauma, early detection and treatment of pneumothorax are vital. Chest radiography in these patients is limited to anteroposterior (AP) supine films, in which radiographic features of pneumothorax may be quite subtle. Hence, rapid and accurate bedside ultrasonography can expedite resuscitation. Sonographic features of pneumothorax have been identified in a number of studies. The technique involves identification of the pleural line and observation for features such as “lung sliding” and comet‐tail artifacts, which are absent in pneumothorax. Based on a review of the literature, the author describes these features and discusses the utility of emergency ultrasound in detecting pneumothorax.
Characterization of Benzoyl Coenzyme A Biosynthesis Genes in the Enterocin-Producing Bacterium “
Streptomyces maritimus
”
Authors: Xiang Longkuan , Moore Bradley S. 
Published: January 2003

ABSTRACT

The novel benzoyl coenzyme A (benzoyl-CoA) biosynthesis pathway in “
Streptomyces maritimus
” was investigated through a series of target-directed mutations. Genes involved in benzoyl-CoA formation were disrupted through single-crossover homologous recombination, and the resulting mutants were analyzed for their ability to biosynthesize the benzoyl-CoA-primed polyketide antibiotic enterocin. Inactivation of the unique phenylalanine ammonia-lyase-encoding gene
encP
was previously shown to be absolutely required for benzoyl-CoA formation in “
S. maritimus
”. The fatty acid β-oxidation-related genes
encH
, -
I
, and -
J
, on the other hand, are necessary but not required. In each case, the yield of benzoyl-CoA-primed enterocin dropped below wild-type levels. We attribute the reduced benzoyl-CoA formation in these specific mutants to functional substitution and cross-talk between the products of genes
encH
, -
I
, and -
J
and the enzyme homologues of primary metabolism. Disruption of the benzoate-CoA ligase
encN
gene did not perturb enterocin production, however, demonstrating that
encN
is extraneous and that benzoic acid is not a pathway intermediate. EncN rather serves as a substitute pathway for utilizing exogenous benzoic acid. These experiments provide further support that benzoyl-CoA is formed in a novel bacterial pathway that resembles the eukaryotic assembly of benzoyl-CoA from phenylalanine via a β-oxidative path.
Regulation of theBacillus subtilisHeat Shock GenehtpGIs under Positive Control
Authors: Versteeg Saskia , Escher Angelika , Wende Andy , Wiegert Thomas , Schumann Wolfgang 
Published: January 2003

ABSTRACTThe heat shock genes ofBacillus subtilisare assigned to four classes on the basis of their regulation mechanisms. While classes I and III are negatively controlled by two different transcriptional repressors, class II is regulated by the alternative sigma factor σB. All heat shock genes with unidentified regulatory mechanisms, among themhtpG, constitute class IV. Here, we show that expression ofhtpGis under positive control. We identified a DNA sequence (GAAAAGG) located downstream of the σA-dependent promoter ofhtpG. The heat inducibility of the promoter could be destroyed by inversion, nucleotide replacements, or removal of this DNA sequence. Fusion of this sequence to the vegetativelepApromoter conferred heat inducibility. Furthermore, we were able to show that the heat induction factor is dependent on the absolute temperature rather than the temperature increment and that nonnative proteins within the cytoplasm fail to inducehtpG.
Characterization of a Novel Intracellular Endopeptidase of the α/β Hydrolase Family from
Streptomyces coelicolor
A3(2)
Authors: Nagy István , Banerjee Tisha , Tamura Tomohiro , Schoofs Geert , Gils Ann , Proost Paul , Tamura Noriko , Baumeister Wolfgang , De Mot René 
Published: January 2003

ABSTRACT

In a proteasome-lacking mutant of
Streptomyces coelicolor
A3(2), an intracellular enzyme with chymotrypsin-like activity, absent from the wild type, was detected. Complementation that restored proteasome function did not suppress expression of the endopeptidase. Since the enzyme was not found in two other
S. coelicolor
proteasome mutants, its expression probably resulted from a secondary mutation arisen in the proteasome mutant. Purification of the endopeptidase revealed its identity to SCO7095, a putative hydrolase encoded by the
S. coelicolor
A3(2) genome with no known homologue. Based on the prediction of a Ser-Asp-His catalytic triad and an α/β hydrolase fold, SCO7095 was assigned to peptidase clan SC. N-terminally His-tagged SCO7095 was efficiently expressed in
Escherichia coli
cells and purified for further characterization. Although SCO7095 is distantly related to several proline iminopeptidases, including
Thermoplasma acidophilum
tricorn-interacting F1, no aminopeptidase activity was detected. On synthetic substrates, the monomeric enzyme exhibited not only chymotrypsin-like activity but also thrombin-like activity.
Functional and Mutational Analysis of Conjugative Transfer Region 2 (Tra2) from the IncHI1 Plasmid R27
Authors: Lawley Trevor D. , Gilmour Matthew W. , Gunton James E. , Tracz Dobryan M. , Taylor Diane E. 
Published: January 2003

ABSTRACTThe transfer 2 region (Tra2) of the conjugative plasmid drR27 (derepressed R27) was analyzed by PSI-BLAST, insertional mutagenesis, genetic complementation, and an H-pilus assay. Tra2 contains 11 mating-pair formation (Mpf) genes that are essential for conjugative transfer, 9 of which are essential for H-pilus production (trhA, -L, -E, -K, -B, -V, -C, -P, and -W). TrhK has similarity to secretin proteins, suggesting a mechanism by which DNA could traverse the outer membrane of donors. The remaining two Mpf genes,trhUandtrhN, play an auxiliary role in H-pilus synthesis and are proposed to be involved in DNA transfer and mating-pair stabilization, respectively. Conjugative transfer abilities were restored for each mutant when complemented with the corresponding transfer gene. In addition to the essential Mpf genes, three genes,trhO,trhZ, andhtdA, modulate R27 transfer frequency. Disruption oftrhOandtrhZseverely reduced the transfer frequencies of drR27, whereas disruption ofhtdAgreatly increased the transfer frequency of wild-type R27 to drR27 levels. A comparison of the essential transfer genes encoded by the Tra2 and Tra1 (T. D. Lawley, M. W. Gilmour, J. E. Gunton, L. J. Standeven, and D. E. Taylor, J. Bacteriol. 184:2173-2183, 2002) of R27 to other transfer systems illustrates that the R27 conjugative transfer system is a chimera composed of IncF-like and IncP-like transfer systems. Furthermore, the Mpf/type IV secretion systems encoded by IncH and IncF transfer systems are distinct from that of the IncP transfer system. The phenotypic and ecological significance of these observations is discussed.
Accumulation ofS-Adenosyl-l-Methionine Enhances Production of Actinorhodin but Inhibits Sporulation inStreptomyces lividansTK23
Authors: Kim Dong-Jin , Huh Jung-Hyun , Yang Young-Yell , Kang Choong-Min , Lee In-Hyung , Hyun Chang-Gu , Hong Soon-Kwang , Suh Joo-Won 
Published: January 2003

ABSTRACTS-Adenosyl-l-methionine synthetase (SAM-s) catalyzes the biosynthesis of SAM from ATP andl-methionine. Despite extensive research with many organisms, its role inStreptomycessp. remains unclear. In the present study, the putative SAM-s gene was isolated from a spectinomycin producer,Streptomyces spectabilis. The purified protein from the transformedEscherichia coliwith the isolated gene synthesized SAM froml-methionine and ATP in vitro, strongly indicating that the isolated gene indeed encoded the SAM-s protein. The overexpression of the SAM-s gene inStreptomyces lividansTK23 inhibited sporulation and aerial mycelium formation but enhanced the production of actinorhodin in both agar plates and liquid media. Surprisingly, the overexpressed SAM was proven by Northern analysis to increase the production of actinorhodin through the induction ofactII-ORF4, a transcription activator of actinorhodin biosynthetic gene clusters. In addition, we found that a certain level of intracellular SAM is critical for the induction of antibiotic biosynthetic genes, since the control strain harboring only the plasmid DNA did not show any induction ofactII-ORF4 until it reached a certain level of SAM in the cell. From these results, we concluded that the SAM plays important roles as an intracellular factor in both cellular differentiation and antibiotic production inStreptomycessp.
Escherichia coliCells with Increased Levels of DnaA and Deficient in Recombinational Repair Have Decreased Viability
Authors: Grigorian Aline V. , Lustig Rachel B. , Guzmán Elena C. , Mahaffy Joseph M. , Zyskind Judith W. 
Published: January 2003

ABSTRACTThednaAoperon ofEscherichia colicontains the genesdnaA,dnaN, andrecFencoding DnaA, β clamp of DNA polymerase III holoenzyme, and RecF. When the DnaA concentration is raised, an increase in the number of DNA replication initiation events but a reduction in replication fork velocity occurs. Because DnaA is autoregulated, these results might be due to the inhibition ofdnaNandrecFexpression. To test this, we examined the effects of increasing the intracellular concentrations of DnaA, β clamp, and RecF, together and separately, on initiation, the rate of fork movement, and cell viability. The increased expression of one or more of thednaAoperon proteins had detrimental effects on the cell, except in the case of RecF expression. A shorter C period was not observed with increased expression of the β clamp; in fact, many chromosomes did not complete replication in runout experiments. Increased expression of DnaA alone resulted in stalled replication forks, filamentation, and a decrease in viability. When the three proteins of thednaAoperon were simultaneously overexpressed, highly filamentous cells were observed (>50 μm) with extremely low viability and, in runout experiments, most chromosomes had not completed replication. The possibility that recombinational repair was responsible for the survival of cells overexpressing DnaA was tested by using mutants in different recombinational repair pathways. The absence of RecA, RecB, RecC, or the proteins in the RuvABC complex caused an additional ∼100-fold drop in viability in cells with increased levels of DnaA, indicating a requirement for recombinational repair in these cells.
clpPofStreptococcus salivariusIs a Novel Member of the Dually Regulated Class of Stress Response Genes in Gram-Positive Bacteria
Authors: Chastanet Arnaud , Msadek Tarek 
Published: January 2003

ABSTRACTNucleotide sequence analysis of theStreptococcus salivarius clpPlocus revealed potential binding sites for both the CtsR and HrcA repressors. Dual regulation by HrcA and CtsR was demonstrated by usingBacillus subtilisas a heterologous host, and CtsR was shown to bind directly to theclpPpromoter sequence. This is the first example of aclpPgene under the control of HrcA.
Osmotic Stress Signaling and Osmoadaptation in Yeasts
Authors: Hohmann Stefan 
Published: January 2003

SUMMARY
The ability to adapt to altered availability of free water is a fundamental property of living cells. The principles underlying osmoadaptation are well conserved. The yeast Saccharomyces cerevisiae is an excellent model system with which to study the molecular biology and physiology of osmoadaptation. Upon a shift to high osmolarity, yeast cells rapidly stimulate a mitogen-activated protein (MAP) kinase cascade, the high-osmolarity glycerol (HOG) pathway, which orchestrates part of the transcriptional response. The dynamic operation of the HOG pathway has been well studied, and similar osmosensing pathways exist in other eukaryotes. Protein kinase A, which seems to mediate a response to diverse stress conditions, is also involved in the transcriptional response program. Expression changes after a shift to high osmolarity aim at adjusting metabolism and the production of cellular protectants. Accumulation of the osmolyte glycerol, which is also controlled by altering transmembrane glycerol transport, is of central importance. Upon a shift from high to low osmolarity, yeast cells stimulate a different MAP kinase cascade, the cell integrity pathway. The transcriptional program upon hypo-osmotic shock seems to aim at adjusting cell surface properties. Rapid export of glycerol is an important event in adaptation to low osmolarity. Osmoadaptation, adjustment of cell surface properties, and the control of cell morphogenesis, growth, and proliferation are highly coordinated processes. The Skn7p response regulator may be involved in coordinating these events. An integrated understanding of osmoadaptation requires not only knowledge of the function of many uncharacterized genes but also further insight into the time line of events, their interdependence, their dynamics, and their spatial organization as well as the importance of subtle effects.