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Susan Jones

Publications and source records attributed to Susan Jones.

At least 19 recordsLinked to original sources
PubMed2007

Protein-RNA interactions: structural analysis and functional classes.

A data set of 89 protein-RNA complexes has been extracted from the Protein Data Bank, and the nucleic acid recognition sites characterized through direct contacts, accessible surface area, and secondary structure motifs. The differences between RNA recognition sites that bind to RNAs in functional classes has also been analyzed. Analysis of the complete data set revealed that van der Waals interactions are more numerous than hydrogen bonds and the contacts made to the nucleic acid backbone occur more frequently than specific contacts to nucleotide bases. Of the base-specific contacts that were observed, contacts to guanine and adenine occurred most frequently. The most favored amino acid-nucleotide pairings observed were lysine-phosphate, tyrosine-uracil, arginine-phosphate, phenylalanine-adenine and tryptophan-guanine. The amino acid propensities showed that positively charged and polar residues were favored as expected, but also so were tryptophan and glycine. The propensities calculated for the functional classes showed trends similar to those observed for the complete data set. However, the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts than the expected. Hence, whilst the types of amino acids involved in the interfaces are similar, the distribution of specific contacts is dependent upon the functional class of the RNA bound.

Amino Acid Motifs↗
PubMed2006

SHARP2: protein-protein interaction predictions using patch analysis.

UNLABELLED: SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein-protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion (SHARP2). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHARP2 enables users to upload 3D protein structure files in PDB format, to obtain information on potential interaction sites as downloadable HTML tables and to view the location of the sites on the 3D structure using Jmol. The server allows for the input of multiple structures and multiple combinations of parameters. Therefore predictions can be made for complete datasets, as well as individual structures. AVAILABILITY: http://www.bioinformatics.sussex.ac.uk/SHARP2.

Algorithms↗
PubMed2006

A systematic study of the effect of physiological factors on beta2-microglobulin amyloid formation at neutral pH.

Beta(2)-microglobulin (beta(2)m) forms amyloid fibrils that deposit in the musculo-skeletal system in patients undergoing long-term hemodialysis. How beta(2)m self-assembles in vivo is not understood, since the monomeric wild-type protein is incapable of forming fibrils in isolation in vitro at neutral pH, while elongation of fibril-seeds made from recombinant protein has only been achieved at low pH or at neutral pH in the presence of detergents or cosolvents. Here we describe a systematic study of the effect of 11 physiologically relevant factors on beta(2)m fibrillogenesis at pH 7.0 without denaturants. By comparing the results obtained for the wild-type protein with those of two variants (DeltaN6 and V37A), the role of protein stability in fibrillogenesis is explored. We show that DeltaN6 forms low yields of amyloid-like fibrils at pH 7.0 in the absence of seeds, suggesting that this species could initiate fibrillogenesis in vivo. By contrast, high yields of amyloid-like fibrils are observed for all proteins when assembly is seeded with fibril-seeds formed from recombinant protein at pH 2.5 stabilized by the addition of heparin, serum amyloid P component (SAP), apolipoprotein E (apoE), uremic serum, or synovial fluid. The results suggest that the conditions within the synovium facilitate fibrillogenesis of beta(2)m and show that different physiological factors may act synergistically to promote fibril formation. By comparing the behavior of wild-type beta(2)m with that of DeltaN6 and V37A, we show that the physiologically relevant factors enhance fibrillogenesis by stabilizing fibril-seeds, thereby allowing fibril extension by rare assembly competent species formed by local unfolding of native monomers.

Amyloid↗
PubMed2006

Pulmonary hypertension in patients with sickle cell disease: a longitudinal study.

UNLABELLED: Although pulmonary hypertension (PHT) is a common complication in patients with sickle cell disease (SCD), the rate of development of PHT and the factors that affect disease progression are unknown. We observed 93 patients over a median follow-up period of 2.6 years (range 0.2-5.1 years). Data were censored at the time of death or loss to follow-up. Pulmonary hypertension was associated with an increased risk of death (relative risk, 9.24; 95% confidence interval: 1.2-73.3; P = 0.01). There was no difference in the risk of death when patients with different degrees of PHT were compared. Lactate dehydrogenase and blood urea nitrogen were significantly associated with PHT in a logistic regression model. Higher levels of fetal haemoglobin and treatment with hydroxycarbamide were observed more frequently in patients without PHT. Thirteen per cent of patients with no previous evidence of PHT developed PHT following 3 years of observation. IN CONCLUSION: (1) PHT, regardless of severity, is associated with an increased risk of death in SCD patients; (2) haemolysis is strongly associated with PHT in SCD; (3) high levels of fetal haemoglobin and hydroxycarbamide therapy may decrease the occurrence of PHT; (4) screening for PHT is indicated for SCD patients in their non-crisis, steady states.

Adult↗
PubMed2006

Diagnosing and treating benign paroxysmal positional vertigo.

Gerontological nurses play a critical role in the early recognition of benign paroxysmal positional vertigo (BPPV), a condition that accounts for approximately 50% of vertigo in older adults. BPPV results in vertigo when debris collects in one or more of the semicircular canals, most typically the posterior canal. It may be differentiated from other forms of vertigo because it results in dizziness when recumbent or with head position changes. BPPV may be successfully treated with repositioning therapy, such as the Epley maneuver. Nurses working in medical offices, longterm care facilities, and assisted living may be called on to perform this maneuver. Gerontological nurses play a key role in assessing and treating BPPV, therefore minimizing unnecessary testing and medication and reducing the suffering and expense for patients with this condition.

Aged↗
PubMed2005

Functional NR2B- and NR2D-containing NMDA receptor channels in rat substantia nigra dopaminergic neurones.

NMDA receptors regulate burst firing of dopaminergic neurones in the substantia nigra pars compacta (SNc) and may contribute to excitotoxic cell death in Parkinson's disease (PD). In order to investigate the subunit composition of functional NMDA receptors in identified rat SNc dopaminergic neurones, we have analysed the properties of individual NMDA receptor channels in outside-out patches. NMDA (100 nm) activated channels corresponding to four chord conductances of 18, 30, 41 and 54 pS. Direct transitions were observed between all conductance levels. Between 18 pS and 41 pS conductance levels, direct transitions were asymmetric, consistent with the presence of NR2D-containing NMDA receptors. Channel activity in response to 100 nm or 200 microm NMDA was not affected by zinc or TPEN (N,N,N',N'-tetrakis-[2-pyridylmethyl]-ethylenediamine), indicating that SNc dopaminergic neurones do not contain functional NR2A subunits. The effect of the NR2B antagonist ifenprodil was complex: 1 microm ifenprodil reduced open probability, while 10 microm reduced channel open time but had no effect on open probability of channels activated by 100 nm NMDA. When the concentration of NMDA was increased to 200 microm, ifenprodil (10 microm) produced the expected reduction in open probability. These results indicate that NR2B subunits are present in SNc dopaminergic neurones. Taken together, these findings indicate that NR2D and NR2B subunits form functional NMDA receptor channels in SNc dopaminergic neurones, and suggest that they may form a triheteromeric NMDA receptor composed of NR1/NR2B/NR2D subunits.

Animals↗
PubMed2005

Phenotypic variation between parent-offspring trios and non-trios in genetic studies of schizophrenia.

BACKGROUND: Phenotypic differences between parent-offspring trios and non-trios have been reported for various psychiatric disorders, and it has been suggested that this may make comparisons of case-control and family-based results for gene-disease association studies inappropriate. AIMS: To compare phenotypes between trios and non-trios with schizophrenia, and explore possible reasons for differences observed. METHOD: Phenotypes were compared between trios (n=75) and non-trios (n=424) collected as part of a case-control study. RESULTS: Differences were observed for most phenotypes investigated, although all were eliminated after adjusting for confounding. CONCLUSIONS: Confounding, genetic heterogeneity or selection bias could result in differences in case-control and family-based results. However as we discuss, where adequately designed case-control studies are used, gene-disease association results would be incomparable between family-based and case-control studies only if genetic heterogeneity was present. These results do not support the presence of such genetic heterogeneity in schizophrenia.

Adolescent↗
PubMed2005

Prevalence and significance of neurocognitive dysfunction in hepatitis C in the absence of correlated risk factors.

Neurocognitive morbidity has been reported in individuals with chronic hepatitis C virus (HCV) infection, but the magnitude of such dysfunction in the absence of disease-correlated factors known to affect the central nervous system (e.g., substance abuse, cirrhosis, depression, interferon treatment) and the impact of any such change on functioning is unclear. We investigated a cohort of individuals with HCV, all of whom were carefully screened to exclude relevant comorbidities, to elucidate virus-related changes in the brain using neuropsychological tests and magnetic resonance spectroscopy (MRS). A cohort of 37 patients with chronic HCV infection was culled from 300 consecutive patients presenting to a tertiary care liver clinic. A comparison group of healthy controls (n = 46) was also assessed. Of 10 neurocognitive measures evaluated, the HCV group showed marginally poorer learning efficiency compared with controls; only 13% of patients demonstrated a clinical level of impairment on this test (defined as 1.5 SD below the normative standard). Although patients reported greater levels of fatigue and symptoms of depression, these factors did not correlate with the degree of learning inefficiency. With respect to MRS, the HCV group demonstrated increased choline and reduced N-acetyl aspartate relative to controls in the central white matter. Indicators of liver disease severity did not correlate with either memory or MRS abnormalities. In conclusion, while our findings support an association between hepatitis C and indicators of central nervous system involvement in a cohort of patients carefully screened to eliminate other factors influencing neurocognitive integrity, the clinical significance of these effects is limited.

Adult↗
PubMed2005

Synaptic plasticity and drug addiction.

Recent studies have suggested that the development of addictive behaviours shares common features with traditional learning models. Synaptic plasticity, a possible substrate for learning, has been demonstrated in neural reward circuits and might contribute to the learning of addictive behaviours. Changes in the strength of synaptic connections have been investigated in dopaminergic cells of the ventral tegmental area in response to several addictive drugs. Rapid and persistent forms of synaptic plasticity (specifically, long-lasting synaptic potentiation) have been demonstrated to accompany some of the behavioural effects of addictive drugs. We hypothesize that drug-induced synaptic plasticity might play a role in reward-related learning and addiction by modifying the fine tuning of dopaminergic cell firing.

Brain↗
PubMed2005

Pediatric major resuscitation--respiratory compromise as a criterion for mandatory surgeon presence.

UNLABELLED: The American College of Surgeons Committee on Trauma has indicated that there are minimum criteria for a trauma surgeon to respond to a major resuscitation (MR) within 15 minutes. These criteria have been required for children without significant data to support their validity. Our hypothesis is that prehospital intubation/respiratory compromise (IRC) as a criterion to define an MR will be an accurate predictor. METHODS: The trauma registry of a level I trauma center was used for data collection of age, injury severity score (ISS), IRC, mortality, hospital days, intensive care unit (ICU) days, and emergency operations. Chi2 with Yates correction and Mann-Whitney rank-sum testing was used for statistical analysis expressed as mean +/- SEM. RESULTS: One hundred eighteen patients were encoded as MR. Forty patients had prehospital IRC and 78 patients did not. There were statistically significant differences seen in ISS, ICU length of stay, and mortality (P < .001). Forty-five percent of patients with IRC died. None of the patients without IRC died. CONCLUSION: Injured children with prehospital IRC are significantly more likely to die, have a higher ISS, and a longer ICU length of stay. Prehospital respiratory distress in injured children in our trauma system is a reasonable criterion to define an MR in children.

Child↗
PubMed2005

A similar impairment in CA3 mossy fibre LTP in the R6/2 mouse model of Huntington's disease and in the complexin II knockout mouse.

Complexin II is reduced in Huntington's disease (HD) patients and in the R6/2 mouse model of HD. Mice lacking complexin II (Cplx2-/- mice) show selective cognitive deficits that reflect those seen in R6/2 mice. To determine whether or not there is a common mechanism that might underlie the cognitive deficits, long-term potentiation (LTP) was examined in the CA3 region of hippocampal slices from R6/2 mice and Cplx2-/- mice. While associational/commissural (A/C) LTP was not significantly different, mossy fibre (MF) LTP was significantly reduced in slices from R6/2 mice and Cplx2-/- mice compared with wild-type (WT) and Cplx2+/+ control mice. MF field excitatory postsynaptic potentials (fEPSPs) in response to paired stimuli were not significantly different between control mice and R6/2 or Cplx2-/- mice, suggesting that MF basal glutamate release is unaffected. Forskolin (30 microm) caused an increase in glutamate release at MF synapses in slices from R6/2 mice and from Cplx2-/- mice that was not significantly different from that seen in control mice, indicating that the capacity for increased glutamate release is not diminished. Thus, R6/2 mice and Cplx2-/- mice have a common selective impairment of MF LTP in the CA3 region. Together, these data suggest that complexin II is required for MF LTP, and that depletion of complexin II causes a selective impairment in MF LTP in the CA3 region. This impairment in MF LTP could contribute to spatial learning deficits observed in R6/2 and Cplx2-/- mice.

2-Amino-5-phosphonovalerate↗
PubMed2005

Molecular determinants for PspA-mediated repression of the AAA transcriptional activator PspF.

The Escherichia coli phage shock protein system (pspABCDE operon and pspG gene) is induced by numerous stresses related to the membrane integrity state. Transcription of the psp genes requires the RNA polymerase containing the sigma(54) subunit and the AAA transcriptional activator PspF. PspF belongs to an atypical class of sigma(54) AAA activators in that it lacks an N-terminal regulatory domain and is instead negatively regulated by another regulatory protein, PspA. PspA therefore represses its own expression. The PspA protein is distributed between the cytoplasm and the inner membrane fraction. In addition to its transcriptional inhibitory role, PspA assists maintenance of the proton motive force and protein export. Several lines of in vitro evidence indicate that PspA-PspF interactions inhibit the ATPase activity of PspF, resulting in the inhibition of PspF-dependent gene expression. In this study, we characterize sequences within PspA and PspF crucial for the negative effect of PspA upon PspF. Using a protein fragmentation approach, we show that the integrity of the three putative N-terminal alpha-helical domains of PspA is crucial for the role of PspA as a negative regulator of PspF. A bacterial two-hybrid system allowed us to provide clear evidence for an interaction in E. coli between PspA and PspF in vivo, which strongly suggests that PspA-directed inhibition of PspF occurs via an inhibitory complex. Finally, we identify a single PspF residue that is a binding determinant for PspA.

Bacterial Proteins↗
PubMed2004

Pulmonary hypertension in sickle cell disease.

BACKGROUND: Recurrent vaso-occlusive episodes lead to progressive end-organ damage in patients with sickle cell disease. We sought to determine the prevalence of pulmonary hypertension in adult patients with sickle cell disease and to identify factors associated with this life-threatening complication. METHODS: Sixty patients (> or =18 years of age; mean [+/- SD] age, 37 +/- 13 years) followed at a University Medical Center were evaluated. They were selected by a systematic sampling of patients presenting to the clinic for routine follow-up visits. All enrolled subjects underwent a clinical examination, Doppler echocardiography, pulmonary function tests, and hematologic tests during a single visit. Pulmonary hypertension was defined using an age- and body mass index-adjusted nomogram. RESULTS: The prevalence of pulmonary hypertension was 30% (18/60). Ten patients had mild pulmonary hypertension (up to 44 mm Hg), 5 had moderate pulmonary hypertension (45 to 74 mm Hg), and 2 had severe pulmonary hypertension (> or =75 mm Hg). In a logistic regression model, both lower fetal hemoglobin level and lower systolic blood pressure were associated with the presence of pulmonary hypertension. CONCLUSION: We found that the prevalence of pulmonary hypertension in adult patients with sickle cell disease was substantial, particularly in those with lower levels of fetal hemoglobin and lower systolic blood pressure.

Adult↗
PubMed2004

Determination of protein charge by capillary zone electrophoresis.

The feasibility of employing classical electrophoresis theory to determine the net charge (valence) of proteins by capillary zone electrophoresis is illustrated in this paper. An outline of a procedure to facilitate the interpretation of mobility measurements is demonstrated by its application to a published mobility measurement for Staphylococcal nuclease at pH 8.9 that had been obtained by capillary zone electrophoresis. The significantly higher valence of +7.5 (cf. 5.6 from the same series of measurements) that has been reported on the basis of a "charge ladder" approach for charge determination signifies the likelihood that the latter generic approach may be prone to error arising from nonconformity of the experimental system with an inherent assumption that chemical modification or mutation of amino acid residues has no effect on the overall three-dimensional size and shape of the protein.

Electrophoresis, Capillary↗
PubMed2004

Habitat disturbance and the diversity and abundance of ants (Formicidae) in the Southeastern Fall-Line Sandhills.

We examined habitat disturbance, species richness, equitability, and abundance of ants in the Fall-Line Sandhills, at Fort Benning, Georgia. We collected ants with pitfall traps, sweep nets, and by searching tree trunks. Disturbed areas were used for military training; tracked and wheeled vehicles damaged vegetation and soils. Highly disturbed sites had fewer trees, diminished ground cover, warmer soils in the summer, and more compacted soils with a shallower A-horizon. We collected 48 species of ants, in 23 genera (141,468 individuals), over four years of sampling. Highly disturbed areas had fewer species, and greater numbers of ants than did moderately or lightly disturbed areas. The ant communities in disturbed areas were also less equitable, and were dominated by Dorymyrmex smithi.

Animals↗
PubMed2004

Identifying DNA-binding proteins using structural motifs and the electrostatic potential.

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix-turn-helix (HTH), helix-hairpin-helix (HhH) and helix-loop-helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif.

Amino Acid Motifs↗
PubMed2004

An overview of the basic helix-loop-helix proteins.

The basic helix-loop-helix proteins are dimeric transcription factors that are found in almost all eukaryotes. In animals, they are important regulators of embryonic development, particularly in neurogenesis, myogenesis, heart development and hematopoiesis.

Animals↗