bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleic Acid Binding-Induced Gag Dimerization in the Assembly of Rous Sarcoma Virus Particles In Vitro
Authors: Ma Yu May , Vogt Volker M. 
Published: December 2003

ABSTRACT
As also found for other retroviruses, the Rous sarcoma virus structural protein Gag is necessary and sufficient for formation of virus-like particles (VLPs). Purified polypeptide fragments comprising most of Gag spontaneously assemble in vitro at pH 6.5 into VLPs lacking a membrane, a process that requires nucleic acid. We showed previously that the minimum length of a DNA oligonucleotide that can support efficient assembly is 16 nucleotides (nt), twice the protein's binding site size. This observation suggests that the essential role of nucleic acid in assembly is to promote the formation of Gag dimers. In order to gain further insight into the role of dimerization, we have studied the assembly properties of two proteins, a nearly full-length Gag (ΔMBDΔPR) capable of proper in vitro assembly and a smaller Gag fragment (CTD-NC) capable of forming only irregular aggregates but with the same pH and oligonucleotide length requirements as for assembly with the larger protein. In analyses by sedimentation velocity and by cross-linking, both proteins remained monomeric in the absence of oligonucleotides or in the presence of an oligonucleotide of length 8 nt (GT8). At pH 8, which does not support assembly, binding to GT16 induced the formation of dimers of ΔMBDΔPR but not of CTD-NC, implying that dimerization requires the N-terminal domain of the capsid moiety of Gag. Assembly of VLPs was induced by shifting the pH of dimeric complexes of ΔMBDΔPR and GT16 from 8 to 6.5. An analogue of GT16 with a ribonucleotide linkage in the middle also supported dimer formation at pH 8. Even after quantitative cleavage of the oligonucleotide by treatment of the complex with RNase, these dimers could be triggered to undergo assembly by pH change. This result implies that protein-protein interactions stabilize the dimer. We propose that binding of two adjacent Gag molecules on a stretch of nucleic acid leads to protein-protein interactions that create a Gag dimer and that this species has an exposed surface not present in monomers which allows polymerization of the dimers into a spherical shell.
Intrapatient Alterations in the Human Immunodeficiency Virus Type 1 gp120 V1V2 and V3 Regions Differentially Modulate Coreceptor Usage, Virus Inhibition by CC/CXC Chemokines, Soluble CD4, and the b12 and 2G12 Monoclonal Antibodies
Authors: Nabatov Alexey A. , Pollakis Georgios , Linnemann Thomas , Kliphius Aletta , Chalaby Moustapha I. M. , Paxton William A. 
Published: December 2003

ABSTRACT
We studied human immunodeficiency virus type 1 (HIV-1) chimeric viruses altering in their gp120 V1V2 and V3 envelope regions to better map which genetic alterations are associated with specific virus phenotypes associated with HIV-1 disease progression. The V1V2 and V3 regions studied were based on viruses isolated from an individual with progressing HIV-1 disease. Higher V3 charges were linked with CXCR4 usage, but only when considered within a specific V1V2 and V3 N-linked glycosylation context. When the virus gained R5X4 dual tropism, irrespective of its V3 charge, it became highly resistant to inhibition by RANTES and highly sensitive to inhibition by SDF-1α. R5 viruses with higher positive V3 charges were more sensitive to inhibition by RANTES, while R5X4 dualtropic viruses with higher positive V3 charges were more resistant to inhibition by SDF-1α. Loss of the V3 N-linked glycosylation event rendered the virus more resistant to inhibition by SDF-1α. The same alterations in the V1V2 and V3 regions influenced the extent to which the viruses were neutralized with soluble CD4, as well as monoclonal antibodies b12 and 2G12, but not monoclonal antibody 2F5. These results further identify a complex set of alterations within the V1V2 and V3 regions of HIV-1 that can be selected in the host via alterations of coreceptor usage, CC/CXC chemokine inhibition, CD4 binding, and antibody neutralization.
Mosaic Evolution of the Severe Acute Respiratory Syndrome Coronavirus
Authors: Stavrinides John , Guttman David S. 
Published: December 2003

ABSTRACTSevere acute respiratory syndrome (SARS) is a deadly form of pneumonia caused by a novel coronavirus, a viral family responsible for mild respiratory tract infections in a wide variety of animals including humans, pigs, cows, mice, cats, and birds. Analyses to date have been unable to identify the precise origin of the SARS coronavirus. We used Bayesian, neighbor-joining, and split decomposition phylogenetic techniques on the SARS virus replicase, surface spike, matrix, and nucleocapsid proteins to reveal the evolutionary origin of this recently emerging infectious agent. The analyses support a mammalian-like origin for the replicase protein, an avian-like origin for the matrix and nucleocapsid proteins, and a mammalian-avian mosaic origin for the host-determining spike protein. A bootscan recombination analysis of the spike gene revealed high nucleotide identity between the SARS virus and a feline infectious peritonitis virus throughout the gene, except for a 200- base-pair region of high identity to an avian sequence. These data support the phylogenetic analyses and suggest a possible past recombination event between mammalian-like and avian-like parent viruses. This event occurred near a region that has been implicated to be the human receptor binding site and may have been directly responsible for the switch of host of the SARS coronavirus from animals to humans.
Alternative Polyadenylation of Adeno-Associated Virus Type 5 RNA within an Internal Intron Is Governed by both a Downstream Element within the Intron 3′ Splice Acceptor and an Element Upstream of the P41 Initiation Site
Authors: Qiu Jianming , Nayak Ramnath , Pintel David J. 
Published: December 2003

ABSTRACT

Adeno-associated virus type 5 (AAV5) has a linear, single-stranded DNA genome of ca. 5 kb and an overlapping transcription profile featuring multiple promoters and a single intron in the center of the genome. Unlike the situation for the prototype AAV2, AAV5 RNAs transcribed from upstream promoters at map units 7 (P7) and 19 (P19), which encode the viral Rep proteins, are predominantly polyadenylated at a site within the intron [(pA)p]. RNAs generated from the AAV5 capsid gene promoter P41, which is only 78 nucleotides (nt) upstream of the intron donor, and 281 nt upstream of (pA)p, primarily readthrough (pA)p, are polyadenylated at a more distal site at the 3′ end of the genome [(pA)d] and ultimately spliced. The intron contains the core sequences sufficient for polyadenylation at (pA)p, which is governed by a G/U-rich downstream element that overlaps with the intron 3′ A2 splice acceptor. In addition, polyadenylation of P7- and P19-generated RNAs at (pA)p is influenced by an upstream element that lies 5′ to the start of the P41 transcript. Our results also suggest that splicing and polyadenylation of P41-generated RNA can compete for the same pool of precursor pre-mRNA molecules. The
cis
-acting signals within the A2 3′ splice site that govern polyadenylation and splicing of AAV5 RNAs must be optimized to program both (i) the levels of polyadenylation of P7- and P19-generated RNA at (pA)p required to generate the proper levels of the essential Rep proteins and (ii) the splicing of P41-generated RNAs to generate the proper ratio of capsid proteins during AAV5 infection.
CcpA-Dependent Carbon Catabolite Repression in Bacteria
Authors: Warner Jessica B. , Lolkema Juke S. 
Published: December 2003

SUMMARY
Carbon catabolite repression (CCR) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. In gram-positive bacteria, CcpA-dependent CCR is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate HPr at a serine residue at the expense of ATP. The reaction is catalyzed by HPr kinase, which is activated by glycolytic intermediates. In this review, the distribution of CcpA-dependent CCR among bacteria is investigated by searching the public databases for homologues of HPr kinase and HPr-like proteins throughout the bacterial kingdom and by analyzing their properties. Homologues of HPr kinase are commonly observed in the phylum Firmicutes but are also found in the phyla Proteobacteria, Fusobacteria, Spirochaetes, and Chlorobi, suggesting that CcpA-dependent CCR is not restricted to gram-positive bacteria. In the α and β subdivisions of the Proteobacteria, the presence of HPr kinase appears to be common, while in the γ subdivision it is more of an exception. The genes coding for the HPr kinase homologues of the Proteobacteria are in a gene cluster together with an HPr-like protein, termed XPr, suggesting a functional relationship. Moreover, the XPr proteins contain the serine phosphorylation sequence motif. Remarkably, the analysis suggests a possible relation between CcpA-dependent gene regulation and the nitrogen regulation system (Ntr) found in the γ subdivision of the Proteobacteria. The relation is suggested by the clustering of CCR and Ntr components on the genome of members of the Proteobacteria and by the close phylogenetic relationship between XPr and NPr, the HPr-like protein in the Ntr system. In bacteria in the phylum Proteobacteria that contain HPr kinase and XPr, the latter may be at the center of a complex regulatory network involving both CCR and the Ntr system.
Bioprospecting for Microbial Endophytes and Their Natural Products
Authors: Strobel Gary , Daisy Bryn 
Published: December 2003

SUMMARY
Endophytic microorganisms are to be found in virtually every plant on earth. These organisms reside in the living tissues of the host plant and do so in a variety of relationships, ranging from symbiotic to slightly pathogenic. Because of what appears to be their contribution to the host plant, the endophytes may produce a plethora of substances of potential use to modern medicine, agriculture, and industry. Novel antibiotics, antimycotics, immunosuppressants, and anticancer compounds are only a few examples of what has been found after the isolation, culture, purification, and characterization of some choice endophytes in the recent past. The potential prospects of finding new drugs that may be effective candidates for treating newly developing diseases in humans, plants, and animals are great.
Molecular Basis of Bacterial Outer Membrane Permeability Revisited
Authors: Nikaido Hiroshi 
Published: December 2003

SUMMARYGram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.
RNA Interference: Biology, Mechanism, and Applications
Authors: Agrawal Neema , Dasaradhi P. V. N. , Mohmmed Asif , Malhotra Pawan , Bhatnagar Raj K. , Mukherjee Sunil K. 
Published: December 2003

SUMMARY
Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.
A Continuum of Anionic Charge: Structures and Functions ofd-Alanyl-Teichoic Acids in Gram-Positive Bacteria
Authors: Neuhaus Francis C. , Baddiley James 
Published: December 2003

SUMMARYTeichoic acids (TAs) are major wall and membrane components of most gram-positive bacteria. With few exceptions, they are polymers of glycerol-phosphate or ribitol-phosphate to which are attached glycosyl andd-alanyl ester residues. Wall TA is attached to peptidoglycan via a linkage unit, whereas lipoteichoic acid is attached to glycolipid intercalated in the membrane. Together with peptidoglycan, these polymers make up a polyanionic matrix that functions in (i) cation homeostasis; (ii) trafficking of ions, nutrients, proteins, and antibiotics; (iii) regulation of autolysins; and (iv) presentation of envelope proteins. The esterification of TAs withd-alanyl esters provides a means of modulating the net anionic charge, determining the cationic binding capacity, and displaying cations in the wall. This review addresses the structures and functions ofd-alanyl-TAs, thed-alanylation system encoded by the dlt operon, and the roles of TAs in cell growth. The importance of dlt in the physiology of many organisms is illustrated by the variety of mutant phenotypes. In addition, advances in our understanding ofd-alanyl ester function in virulence and host-mediated responses have been made possible through targeted mutagenesis of dlt. Studies of the mechanism ofd-alanylation have identified two potential targets of antibacterial action and provided possible screening reactions for designing novel agents targeted tod-alanyl-TA synthesis.
Effects of sodium citrate ingestion before exercise on endurance performance in well trained college runners
Authors: Oöpik V , Saaremets I , Medijainen L , Karelson K , Janson T , Timpmann S 
Published: December 2003

Objective:To test the hypothesis that sodium citrate administered two hours before exercise improves performance in a 5 km running time trial.Methods:A total of 17 male well trained college runners (mean (SD) V̇o2max61.3 (4.9) ml/kg/min) performed a 5 km treadmill run with and without sodium citrate ingestion in a random, double blind, crossover design. In the citrate trial, subjects consumed 1 litre of solution containing 0.5 g of sodium citrate/kg body mass two hours before the run. In the placebo trial, the same amount of flavoured mineral water was consumed.Results:The time required to complete the run was faster in the citrate trial than the placebo trial (1153.2 (74.1) and 1183.8 (91.4) seconds respectively; p = 0.01). Lower packed cell volume and haemoglobin levels were found in venous blood samples taken before and after the run in the citrate compared with the placebo trial. Lactate concentration in the blood sample taken after the run was higher in the citrate than the placebo trial (11.9 (3.0)v9.8 (2.8) mmol/l; p<0.001), and glucose concentration was lower (8.3 (1.9)v8.8 (1.7) mmol/l; p = 0.02).Conclusion:The ingestion of 0.5 g of sodium citrate/kg body mass shortly before a 5 km running time trial improves performance in well trained college runners.
Dynamic force distribution during level walking under the feet of patients with chronic ankle instability
Authors: Nyska M , Shabat S , Simkin A , Neeb M , Matan Y , Mann G 
Published: December 2003

Objectives:To examine changes in the pattern of force transfer between the foot and the floor associated with chronically sprained ankles by measuring the peak forces and their timing under several regions of the feet during level walking.Methods:Twelve young male subjects (mean (SD) age 21 (2) years) with recurrent ankle sprains were studied. Seven of them had unilateral and bilateral chronic instability and laxity, and five had bilateral instability. Twelve healthy men (without orthopaedic or medical disease) served as a control group. Subjects walked at their own pace along a 7 m walkway, which included a Mini-EMED pressure distribution measuring system. The variables measured were relative peak force (fraction of body weight) and relative timing (fraction of stance time). These variables were measured under six regions of interest in each foot print: heel, midfoot, medial, central, and lateral forefoot, and toes.Results:(a) A significant delay to the time of peak force under the central and lateral forefoot and toes in subjects with chronic ankle instability. (b) A significant decrease in the relative forces under the heel and toes and an increase in the relative forces under the midfoot and lateral forefoot in subjects with chronic ankle instability. (c) In the patients with unilateral instability, there were no significant differences in any of the variables between the injured and non-injured foot.Conclusions:In patients with chronic ankle instability, there is a slowing down of weight transfer from heel strike to toe off, a reduced impact at the beginning and end of the stance phase, and a lateral shift of body weight.
Dehydration of football referees during a match
Authors: Da Silva A I , Fernandez R 
Published: December 2003

Objectives:To study hydration status in referees (main) and assistant referees (linesmen) during official football matches.Methods:Twelve male football referees were evaluated; all were volunteers. Before and after each match, the referee and one of the assistants were weighed without clothes and a blood sample was taken. Total water loss was determined for each subject from the change in body weight. The main haematological variables were analysed in the blood samples. Total plasma protein concentration and osmolarity were also determined. Variation in plasma volume was determined from changes in packed cell volume and a combination of changes in packed cell volume and haemoglobin concentrations.Results:During a match, total body water loss was 1.60 (0.13) litres, equivalent to 2.05 (0.18)% of body weight. Body weight was reduced by 1.55 (0.12)%, showing that water ingestion during the interval replaces only 24.4% of the body fluids lost during the match. The assistants lost 0.79 (0.19) litre of water, equivalent to 1.05 (0.25)% of body weight. The referees showed a significant decrease in plasma volume of 4.99 (1.33)%. The assistants showed a non-significant increase in plasma volume. The reduction in plasma volume observed in the referees correlated significantly with total body water loss (r =  0.9623). From these data, it is possible to predict that a dehydration of 1% reflects a reduction in plasma volume of nearly 2.5%.Conclusions:Referees are moderately dehydrated after a football match (2%), whereas assistants show a non-significant dehydration of 1% of their body weight.
Snowblading injuries in Eastern Canada
Authors: Bridges E J , Rouah F , Johnston K M 
Published: December 2003

Objectives:To evaluate injury patterns of snowbladers and compare them with those of skiers and snowboarders. To determine possible effects of helmet use in these sports on injury to the head and neck.Methods:This prospective case series observational study was conducted by collecting the injury reports from the ski patrol during the 1999–2000 season at Mont Tremblant ski resort, Quebec. All participants in downhill winter sports who presented themselves to the ski patrol with traumatic injury related to their sport were included. A concussion was defined as any loss of consciousness, amnesia, confusion, disorientation, vertigo, or headache that resulted from injury. The ski patroller reported helmet use on the accident report at the time of injury.Results:Snowbladers present with a unique pattern of injury compared with skiers and snowboarders. The incidence of leg, knee, and ankle/foot injuries were 20.5%, 25.6%, and 10.3% respectively. Concussions represented 11% of all injuries. There was no increase in other injury, including neck injury, related to helmet use.Conclusions:Unique injury patterns in snowbladers warrant reconsideration of equipment design. Concussion is a common injury on the ski slope. Although the effects of helmet use on concussion rate are inconclusive based on this study, helmet use did not increase the rate of neck injury, even when adjusted for age.
Effects of physical activity on exercise tests and respiratory function
Authors: Cheng Y J , Macera C A , Addy C L , Sy F S , Wieland D , Blair S N 
Published: December 2003

Background:Exercise is an important component of pulmonary rehabilitation for patients with chronic lung disease.Objective:To explore the role of physical activity in maintaining cardiac and respiratory function in healthy people.Methods:Cardiorespiratory fitness was measured by a maximal treadmill test (MTT), and respiratory function was tested by spirometry. The cross sectional study included data from 24 536 healthy persons who were examined at the Cooper Clinic between 1971 and 1995; the longitudinal study included data from 5707 healthy persons who had an initial visit between 1971 and 1995 and a subsequent visit during the next five years. All participants were aged 25–55 years and completed a cardiorespiratory test and a medical questionnaire.Results:In the cross sectional study, after controlling for covariates, being active and not being a recent smoker were associated with better cardiorespiratory fitness and respiratory function in both men and women. In the follow up study, persons who remained or became active had better MTT than persons who remained or became sedentary. Men who remained active had higher forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) than the other groups. Smoking was related to lower cardiorespiratory fitness and respiratory function.Conclusions:Physical activity and non-smoking or smoking cessation is associated with maintenance of cardiorespiratory fitness. Change in physical activity habits is associated with change in cardiorespiratory fitness, but respiratory function contributed little to this association during a five year follow up.