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Biomedical subjects

J B Jones

Publications and source records attributed to J B Jones.

At least 19 recordsLinked to original sources
PubMed2026

Characterization of putatively lytic bacteriophages able to infect Xanthomonas citri subsp. citri and identification of novel putative exopolysaccharide depolymerases.

Asiatic citrus canker (ACC), caused by the Gram-negative bacterium Xanthomonas citri subsp. citri (X. citri), leads to substantial economic losses in the global citrus industry, necessitating sustainable alternatives to conventional copper-based bactericides. In this study, we isolated and sequenced 72 putatively lytic bacteriophages (including 65 previously uncharacterized isolates from São Paulo, Brazil) and characterized their host range, stability and biocontrol potential. Genomic analysis revealed highly successful but low-diversity phage genomic signatures; 70 isolates shared ~95% DNA similarity and were closely related to the Japanese phage CP2, mirroring the clonal nature of the endemic X. citri population. These phages primarily belong to the Autographiviridae family, with the exception of the Schitoviridae isolate XacP77. Using HHsearch and AlphaFold structural modelling, we identified conserved tail-fibre genes predicted to encode putative exopolysaccharide depolymerases with structural homology to carbohydrate-binding modules (CBMs), which may facilitate the degradation of the bacterial xanthan gum capsule during infection. While the phages exhibited robust stability across a wide pH range (4-11) and temperatures up to 55 °C, they were highly sensitive to UV exposure, reaching total inactivation after 160 s. Greenhouse assays demonstrated that treatment with phage P27 reduced ACC lesion production by 60%, pointing to the potential of these viruses and their candidate CBM-containing proteins as components of a sustainable biocontrol development within integrated pest management strategies for X. citri.

Xanthomonas↗
PubMed2005

Relative importance of bacteriocin-like genes in antagonism of Xanthomonas perforans tomato race 3 to Xanthomonas euvesicatoria tomato race 1 strains.

In a previous study, tomato race 3 (T3) strains of Xanthomonas perforans became predominant in fields containing both X. euvesicatoria and X. perforans races T1 and T3, respectively. This apparent ability to take over fields led to the discovery that there are three bacteriocin-like compounds associated with T3 strains. T3 strain 91-118 produces at least three different bacteriocin-like compounds (BCN-A, BCN-B, and BCN-C) antagonistic toward T1 strains. We determined the relative importance of the bacteriocin-like compounds by constructing the following mutant forms of a wild-type (WT) T3 strain to evaluate the antagonism to WT T1 strains: Mut-A (BCN-A-), Mut-B (BCN-B-), Mut-C (BCN-C-), Mut-AB, Mut-BC, and Mut-ABC. Although all mutant and WT T3 strains reduced the T1 populations in in planta growth room experiments, Mut-B and WT T3 were significantly more effective. Mutants expressing BCN-B and either BCN-A or BCN-C reduced T1 populations less than mutants expressing only BCN-A or BCN-C. The triple-knockout mutant Mut-ABC also had a significant competitive advantage over the T1 strain. In pairwise-inoculation field experiments where plants were coinoculated with an individual mutant or WT T3 strain and the T1 strain, the mutant strains and the WT T3 strain were reisolated from more than 70% of the lesions. WT T3 and Mut-B were the most frequently reisolated strains. In field experiments where plants were group inoculated with Mut-A, Mut-B, Mut-C, Mut-ABC, and WT T1 and T3 strains, Mut-B populations dominated all three seasons. In greenhouse and field experiments, the WT and mutant T3 strains had a selective advantage over T1 strains. Bacterial strains expressing both BCN-A and BCN-C appeared to have a competitive advantage over all other mutant and WT strains. Furthermore, BCN-B appeared to be a negative factor, with mutant T3 strains lacking BCN-B having a selective advantage in the field.

Agriculture↗
PubMed2004

Importance of opgHXcv of Xanthomonas campestris pv. vesicatoria in host-parasite interactions.

Tn5 insertion mutants of Xanthomonas campestris pv. vesicatoria were inoculated into tomato and screened for reduced virulence. One mutant exhibited reduced aggressiveness and attenuated growth in planta. Southern blot analyses indicated that the mutant carried a single Tn5 insertion not associated with previously cloned pathogenicity-related genes of X. campestris pv. vesicatoria. The wild-type phenotype of this mutant was restored by one recombinant plasmid (pOPG361) selected from a genomic library of X. campestris pv. vesicatoria 91-118. Tn3-gus insertion mutagenesis and sequence analyses of a subclone of pOPG361 identified a 1,929-bp open reading frame (ORF) essential for complementation of the mutants. The predicted protein encoded by this ORF was highly homologous to the previously reported pathogenicity-related HrpM protein of Pseudomonas syringae pv. syringae and OpgH of Erwinia chrysanthemi. Based on homology, the new locus was designated opgHXcv. Manipulation of the osmotic potential in the intercellular spaces of tomato leaves by addition of mannitol at low concentrations (25 to 50 mM) compensates for the opgHXcv mutation.

Arabidopsis↗
PubMed2004

Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species.

Bacterial blight is an emerging disease that affects primarily onion, but also garlic and Welsh onion. The present study was undertaken to characterize the causative xanthomonad(s) by a polyphasic approach using a worldwide collection of 33 bacterial strains. Analysis of 16S rRNA gene sequence similarities indicated that the causal agent belongs to the campestris core in the genus Xanthomonas, which is in agreement with results of phenotypic characterization (analyses of carbon source utilization and fatty acid methyl esters). However, DNA-DNA hybridization, thermal stability of DNA reassociation and fluorescent amplified fragment length polymorphism analysis allowed the causal agent to be identified as a pathovar of Xanthomonas axonopodis.

Allium↗
PubMed2003

A class of compact dwarf galaxies from disruptive processes in galaxy clusters.

Dwarf galaxies have attracted increased attention in recent years, because of their susceptibility to galaxy transformation processes within rich galaxy clusters. Direct evidence for these processes, however, has been difficult to obtain, with a small number of diffuse light trails and intra-cluster stars being the only signs of galaxy disruption. Furthermore, our current knowledge of dwarf galaxy populations may be very incomplete, because traditional galaxy surveys are insensitive to extremely diffuse or compact galaxies. Aware of these concerns, we recently undertook an all-object survey of the Fornax galaxy cluster. This revealed a new population of compact members, overlooked in previous conventional surveys. Here we demonstrate that these 'ultra-compact' dwarf galaxies are structurally and dynamically distinct from both globular star clusters and known types of dwarf galaxy, and thus represent a new class of dwarf galaxy. Our data are consistent with the interpretation that these are the remnant nuclei of disrupted dwarf galaxies, making them an easily observed tracer of galaxy disruption.

Journal Article↗
PubMed2001

Detection of mitochondrial DNA mutations in pancreatic cancer offers a "mass"-ive advantage over detection of nuclear DNA mutations.

We sequenced the complete 16.5-kb mitochondrial genome (mtDNA) in 15 pancreatic cancer cell lines and xenografts. Homoplasmic mtDNA somatic mutations and novel variants were identified in nearly all samples. Southern blot analysis and direct sequencing of mutation sites showed that the intracellular mass of mtDNA was greatly (6-8-fold) increased in pancreatic cancer cells in relation to corresponding normal cells; this property accounted for and greatly facilitated the identification of these mutations among the dense desmoplastic host reaction characteristic of primary pancreatic cancers. Structural characteristics and mathematical modeling of the evolution of mtDNA mutations suggested that many of the mutations identified might represent a random evolution of homoplasmic variants, rather than necessarily being a product of selective pressures. Complete sequencing of the nuclear MnSOD gene, which protects cells from the mitogenic and toxic effects of oxygen radicals, did not reveal any mutations. Nevertheless, the nearly ubiquitous prevalence and high copy number of mtDNA mutations suggest that they be considered of promising clinical utility in diagnostic applications.

Adenocarcinoma↗
PubMed2001

Pathophysiology of acute pain: implications for clinical management.

To effectively treat acute pain, emergency medicine practitioners must have a thorough understanding of both the pathophysiology and terminology of the pain experience. The pathophysiology of pain is discussed with an emphasis on the mechanisms of acute, inflammatory pain. The various types of pain receptors, pathways and neurotransmitters are also discussed.

Acute Disease↗
PubMed2001

Ethylene-dependent salicylic acid regulates an expanded cell death response to a plant pathogen.

The molecular events associated with susceptible plant responses to disease-causing organisms are not well understood. We have previously shown that ethylene-insensitive tomato plants infected with Xanthomonas campestris pv. vesicatoria have greatly reduced disease symptoms relative to wild-type cultivars. Here we show that salicylic acid (SA) is also an important component of the susceptible disease response. SA accumulates in infected wild-type tissues and is correlated with necrosis but does not accumulate in ethylene-insensitive plants. Exogenous feeding of SA to ethylene-deficient plants restores necrosis, indicating that reduced disease symptoms are associated with failure to accumulate SA. These results indicate a mechanism for co-ordination of phytohormone signals that together constitute a susceptible response to pathogens.

Cell Death↗
PubMed2001

Sublingual hyoscyamine sulfate in combination with ketorolac tromethamine for ureteral colic: a randomized, double-blind, controlled trial.

STUDY OBJECTIVE: We evaluate the safety and efficacy of a single dose of hyoscyamine sulfate in combination with ketorolac tromethamine for the reduction of pain in emergency department patients with ureteral colic. METHODS: We conducted a prospective, randomized, double-blind study at 2 EDs with residency programs in emergency medicine. Patients were at least 18 years old and presented to the ED with an initial history and physical examination consistent with ureteral colic. Patients received a single intravenous dose of 30 mg of ketorolac tromethamine given over a 1-minute period with either a single sublingual dose of 0.125 mg of hyoscyamine sulfate or a placebo. If inadequate analgesia was noted after 30 minutes, a standard dose of meperidine could be administered for rescue. All other treatments including intravenous fluids and antiemetics were standardized. The main study outcome was change in visual analog scale pain score from baseline to 30 minutes. RESULTS: Seventy-two patients were evaluated for inclusion. Thirteen patients who had self-administered pain medications within 4 hours of presentation were excluded before randomization. Sixteen patients who did not have a renal calculus confirmed by either intravenous urogram or helical computed tomography were also excluded from efficacy analysis. There did not appear to be any clinically important differences in the baseline characteristics between the 2 groups. The repeated-measures analysis of the remaining 43 patients showed no clinically important difference in pain score using the visual analog scale at any time point. There were no clinically important differences between the 2 study groups for amount of rescue meperidine administered or end-of-study global satisfaction scores. CONCLUSION: Hyoscyamine sulfate did not provide any additional pain relief from ureteral colic when administered with ketorolac tromethamine. There was no clinically important difference in change of pain scores at 30 minutes in patients with ureteral colic receiving supplemental hyoscyamine sulfate.

Administration, Sublingual↗
PubMed2001

Intravenous administration of prochlorperazine by 15-minute infusion versus 2-minute bolus does not affect the incidence of akathisia: a prospective, randomized, controlled trial.

STUDY OBJECTIVE: We sought to compare the rate of akathisia after administration of intravenous prochlorperazine as a 2-minute bolus or 15-minute infusion. METHODS: We conducted a prospective, randomized, double-blind study in the emergency department of a central-city teaching hospital. Patients aged 18 years or older treated with prochlorperazine for headache, nausea, or vomiting were eligible for inclusion. Study participants were randomized to receive 10 mg of prochlorperazine administered intravenously by means of 2-minute push (bolus group) or 10 mg diluted in 50 mL of normal saline solution administered by means of intravenous infusion during a 15-minute period (infusion group). The main outcome was the number of study participants experiencing akathisia within 60 minutes of administration. Akathisia was defined as either a spontaneous report of restlessness or agitation or a change of 2 or more in the patient-reported akathisia rating scale and a change of at least 1 in the investigator-observed akathisia rating scale. The intensity of headache and nausea was measured with a 100-mm visual analog scale. RESULTS: One hundred patients were enrolled. One study participant was excluded after protocol violation. Seventy-three percent (73/99) of the study participants were treated for headache and 70% (70/99) for nausea. In the bolus group, 26.0% (13/50) had akathisia compared with 32.7% (16/49) in the infusion group (Delta=-6.7%; 95% confidence interval [CI] -24.6% to 11.2%). The difference between the bolus and infusion groups in the percentage of participants who saw a 50% reduction in their headache intensity within 30 minutes was 11.8% (95% CI -9.6% to 33.3%). The difference in the percentage of patients with a 50% reduction in their nausea was 12.6% (95% CI -4.6% to 29.8%). CONCLUSION: A 50% reduction in the incidence of akathisia when prochlorperazine was administered by means of 15-minute intravenous infusion versus a 2-minute intravenous push was not detected. The efficacy of prochlorperazine in the treatment of headache and nausea likewise did not appear to be affected by the rate of administration, although no formal statistical comparisons were made.

Adolescent↗
PubMed2001

Goal orientations and the search for confirmatory affect.

People differ with respect to their beliefs about the consequences of attaining goals. Some people (linkers) believe that attaining certain goals will make them happy, whereas others (nonlinkers) see their happiness as more contingent upon the inherent quality of their actions than upon the outcomes of those actions. Because of the importance linkers place on goal attainment, linkers should be likely to seek information indicative of their progress toward their goals. Because of the importance nonlinkers place on enjoyment, nonlinkers should be likely to seek information indicative of the pleasurableness of their current task. Because negative affect can signal a lack of goal progress, whereas positive affect can signal task enjoyment, linkers may place more weight on their negative than their positive affect, whereas nonlinkers may do the opposite. Consistent with these hypotheses, the results of this study showed that linkers reported more negative affect when exposed to sad videos than when exposed to happy videos but did not report different amounts of positive affect. Nonlinkers, on the other hand, reported more positive affect when exposed to happy videos than when exposed to sad videos but did not report different amounts of negative affect. The implications of this pattern for a number of theoretical perspectives on goals and affect are discussed.

Adult↗
PubMed2001

Reduced expression of the tomato ethylene receptor gene LeETR4 enhances the hypersensitive response to Xanthomonas campestris pv. vesicatoria.

The hypersensitive response (HR) involves rapid death of cells at the site of pathogen infection and is thought to limit pathogen growth through the plant. Ethylene regulates senescence and developmental programmed cell death, but its role in hypersensitive cell death is less clear. Expression of two ethylene receptor genes, NR and LeETR4, is induced in tomato (Lycopersicon esculentum cv. Mill) leaves during an HR to Xanthomonas campestris pv. vesicatoria, with the greatest increase observed in LeETR4. LeETR4 antisense plants previously were shown to exhibit increased sensitivity to ethylene. These plants also exhibit greatly reduced induction of LeETR4 expression during infection and an accelerated HR at inoculum concentrations ranging from 10(5) to 10(7) CFU/ml. Increases in ethylene synthesis and pathogenesis-related gene expression are greater and more rapid in infected LeETR4 antisense plants, indicating an enhanced defense response. Populations of avirulent X. campestris pv. vesicatoria decrease more quickly and to a lower level in the transgenic plants, indicating a greater resistance to this pathogen. Because the ethylene action inhibitor 1-methylcyclopropene alleviates the enhanced HR phenotype in LeETR4 antisense plants, these changes in pathogen response are a result of increased ethylene sensitivity.

Cell Death↗
PubMed2001

Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina.

Tumorigenic Agrobacterium strains isolated from tumours growing on pruned branches of Ficus benjamina have previously been shown to have unique opine metabolism and sufficient 16S rRNA sequence differences to suggest that they belong to a new species. DNA-DNA hybridization results confirmed that these strains represent a new species and Agrobacterium larrymoorei sp. nov. (type strain ATCC 51759T = CFBP 5473T = NCPPB 4096T) is proposed as the name for the species.

DNA, Bacterial↗
PubMed2000

Functional mapping of the MH1 DNA-binding domain of DPC4/SMAD4.

The transcription factor Smad4 binds DNA in response to a TGF-beta ligand-initiated intracellular signaling cascade. SMAD4 is deleted or mutated during tumorigenesis in many human tumors. Some of these mutations occur in the N-terminal portion of the protein, the Mad homology 1 (MH1) region, which exhibits sequence-specific DNA-binding. We used alanine scanning mutagenesis and natural mutations to map the subregion of the MH1 domain necessary for that function. We created 20 individual mutations in the MH1 region of human Smad4 and assayed their effect on DNA-binding in vitro. Mutation of residues in the less conserved N- and C-terminal areas of the MH1 region had no effect on DNA-binding. However, mutations in the domain from L43 to R135 caused a dramatic reduction of the ability of Smad4 to bind DNA. Previous work demonstrated a beta-hairpin protein motif within this region to be responsible for DNA-binding, but suggested that the tumorigenic mutations occurring outside this motif may target a separate function of the MH1 domain. Our results demonstrate that the MH1 domain as a whole is very sensitive to changes in overall structure, and that tumorigenic mutations within the region of L43-R135 indeed would target DNA-binding.

Amino Acid Sequence↗
PubMed2000

Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase(,).

Transition state analogue boronic acid inhibitors mimicking the structures and interactions of good penicillin substrates for the TEM-1 beta-lactamase of Escherchia coli were designed using graphic analyses based on the enzyme's 1.7 A crystallographic structure. The synthesis of two of these transition state analogues, (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1) and (1R)-1-acetamido-2-(3-carboxy-2-hydroxyphenyl)ethylboronic acid (2), is reported. Kinetic measurements show that, as designed, compounds 1 and 2 are highly effective deacylation transition state analogue inhibitors of TEM-1 beta-lactamase, with inhibition constants of 5.9 and 13 nM, respectively. These values identify them as among the most potent competitive inhibitors yet reported for a beta-lactamase. The best inhibitor of the current series was (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1, K(I) = 5.9 nM), which resembles most closely the best known substrate of TEM-1, benzylpenicillin (penicillin G). The high-resolution crystallographic structures of these two inhibitors covalently bound to TEM-1 are also described. In addition to verifying the design features, these two structures show interesting and unanticipated changes in the active site area, including strong hydrogen bond formation, water displacement, and rearrangement of side chains. The structures provide new insights into the further design of this potent class of beta-lactamase inhibitors.

Acylation↗
PubMed2000

Controlled site-selective protein glycosylation for precise glycan structure-catalytic activity relationships.

Glycoproteins occur naturally as complex mixtures of differently glycosylated forms which are difficult to separate. To explore their individual properties, there is a need for homogeneous sources of carbohydrate-protein conjugates and this has recently prompted us to develop a novel method for the site-selective glycosylation of proteins. The potential of the method was illustrated by site-selective glycosylations of subtilisin Bacillus lentus (SBL) as a model protein. A representative library of mono- and disaccharide MTS reagents were synthesized from their parent carbohydrates and used to modify cysteine mutants of SBL at positions 62 in the S2 site, 156 and 166 in the S1 site and 217 in the S1' site. These were the first examples of preparations of homogeneous neoglycoproteins in which both the site of glycosylation and structure of the introduced glycan were predetermined. The scope of this versatile method was expanded further through the combined use of peracetylated MTS reagents and careful pH adjustment to introduce glycans containing different numbers of acetate groups. This method provides a highly controlled and versatile route that is virtually unlimited in the scope of the sites and glycans that may be conjugated, and opens up hitherto inaccessible opportunities for the systematic determination of the properties of glycosylated proteins. This potential has been clearly demonstrated by the determination of detailed glycan structure-hydrolytic activity relationships for SBL. The 48 glycosylated CMMs formed display kcat/KM values that range from 1.1-fold higher than WT to 7-fold lower than WT. The anomeric stereochemistry of the glycans introduced modulates changes in kcat/KM upon acetylation. At positions 62 and 217 acetylation enhances the activity of alpha-glycosylated CMMs but decreases that of beta-glycosylated. This trend is reversed at position 166 where, in contrast, acetylation enhances the kcat/KMs of beta-glycosylated CMMs but decreases those of alpha-glycosylated. Consistent with its surface exposed nature changes at position 156 are more modest, but still allow control of activity, particularly through glycosylation with disaccharide lactose.

Acetylation↗
PubMed2000

Site-selective glycosylation of subtilisin Bacillus lentus causes dramatic increases in esterase activity.

Using site directed mutagenesis combined with chemical modification, we have developed a general and versatile method for the glycosylation of proteins which is virtually unlimited in the scope of proteins and glycans that may be conjugated and in which the site of glycosylation and the nature of the introduced glycan can be carefully controlled. We have demonstrated the applicability of this method through the synthesis of a library of 48 glycosylated forms of the serine protease subtilisin Bacillus lentus (SBL) as single, pure species. As part of our ongoing program to tailor the activity of SBL for use in peptide synthesis, we have screened these enzymes for activity against the esterase substrate succinyl-Ala-Ala-Pro-Phe-S-benzyl. Gratifyingly, 22 enzymes displayed greater than wild type (WT) activity. Glycosylation at positions 62, in the S2 pocket, resulted in five glycosylated forms of SBL that were 1.3- to 1.9-fold more active than WT. At position 217, in the S1' pocket, all glycosylations increased kcat/KM up to a remarkable 8.4-fold greater than WT for the glucosylated enzyme L217C-S-beta-Glc(Ac)3. Furthermore, the ratio of amidase to esterase activity, (kcat/KM)esterase/(kcat/KM)amidase (E/A), is increased relative to wild type for all 48 glycosylated forms of SBL. Again, the most dramatic changes are observed at positions 62 and 217 and L217C-S-beta-Glc(Ac)3 has an E/A that is 17.2-fold greater than WT. The tailored specificity and high activity of this glycoform can be rationalized by molecular modeling analysis, which suggests that the carbohydrate moiety occupies the S1' leaving group pocket and enhances the rate of deacylation of the acyl-enzyme intermediate. These glycosylated enzymes are ideal candidates for use as catalysts in peptide synthesis as they have greatly increased (kcat,KM)esterase and severely reduced (kcat/KM)amidase and will favor the formation of the amide bond over hydrolysis.

Acetylation↗