PubMed Health⌕ Search

Biomedical subjects

I J Alexander

Publications and source records attributed to I J Alexander.

At least 19 recordsLinked to original sources
PubMed2007

FragMatch--a program for the analysis of DNA fragment data.

FragMatch is a user-friendly Java-supported program that automates the identification of taxa present in mixed samples by comparing community DNA fragment data against a database of reference patterns for known species. The program has a user-friendly Windows interface and was primarily designed for the analysis of fragment data derived from terminal restriction fragment length polymorphism analysis of ectomycorrhizal fungal communities, but may be adapted for other applications such as microsatellite analyses. The program uses a simple algorithm to check for the presence of reference fragments within sample files that can be directly imported, and the results appear in a clear summary table that also details the parameters that were used for the analysis. This program is significantly more flexible than earlier programs designed for matching RFLP patterns as it allows default or user-defined parameters to be used in the analysis and has an unlimited database size in terms of both the number of reference species/individuals and the number of diagnostic fragments per database entry. Although the program has been developed with mycorrhizal fungi in mind, it can be used to analyse any DNA fragment data regardless of biological origin. FragMatch, along with a full description and users guide, is freely available to download from the Aberdeen Mycorrhiza Group web page (http://www.aberdeenmycorrhizas.com).

Algorithms↗
PubMed2005

Pine microsatellite markers allow roots and ectomycorrhizas to be linked to individual trees.

Linking roots and ectomycorrhizas (EcM) to individual host trees in the field is required to test whether individual trees support different ectomycorrhizal communities. Here we describe a method that identifies the source of EcM roots by PCR of polymorphic pine nuclear microsatellite loci using fluorescently labelled primers and high-throughput fragment analysis. ITS-PCR can also be performed on the same EcM DNA extract for fungal identification. The method was tested on five neighbouring Scots pine (Pinus sylvestris var scotica) trees in native woodland. Successful host tree identification from DNA extracts of EcM root tips was achieved for 93% of all root fragments recovered from soil cores. It was estimated that each individual mature pine sampled was colonised by between 15 and 19 EcM fungi. The most abundant fungal species were found on all five trees, and within the constraints of the sampling scheme, no differences between trees in EcM fungal community structure or composition were detected.

DNA Fingerprinting↗
PubMed2005

Role of oxalic acid overexcretion in transformations of toxic metal minerals by Beauveria caledonica.

The fungus Beauveria caledonica was highly tolerant to toxic metals and solubilized cadmium, copper, lead, and zinc minerals, converting them into oxalates. This fungus was found to overexcrete organic acids with strong metal-chelating properties (oxalic and citric acids), suggesting that a ligand-promoted mechanism was the main mechanism of mineral dissolution. Our data also suggested that oxalic acid was the main mineral-transforming agent. Cadmium, copper, and zinc oxalates were precipitated by the fungus in the local environment and also in association with the mycelium. The presence of toxic metal minerals often led to the formation of mycelial cords, and in the presence of copper-containing minerals, these cords exhibited enhanced excretion of oxalic acid, which resulted in considerable encrustation of the cords by copper oxalate hydrate (moolooite). It was found that B. caledonica hyphae and cords were covered by a thick hydrated mucilaginous sheath which provided a microenvironment for chemical reactions, crystal deposition, and growth. Cryo-scanning electron microscopy revealed that mycogenic metal oxalates overgrew parental fungal hyphae, leaving a labyrinth of fungal tunnels within the newly formed mineral matter. X-ray absorption spectroscopy revealed that oxygen ligands played a major role in metal coordination within the fungal biomass during the accumulation of mobilized toxic metals by B. caledonica mycelium; these ligands were carboxylic groups in copper phosphate-containing medium and phosphate groups in pyromorphite-containing medium.

Biodegradation, Environmental↗
PubMed2001

Leaf habit influences nitrogen remobilization in Vaccinium species.

The effect of N supply on plant growth and leaf demography of a deciduous and an evergreen Ericaceae was studied in relation to their internal cycling of N. Mature ramets of Vaccinium myrtillus (deciduous) and Vaccinium vitis-idaea (evergreen) were established in sand culture for 1 year with an adequate supply of a balanced nutrient solution. During one growing season, the plants were given two levels of N supply enriched with 15N and eight sequential destructive harvests were taken. Recovery of unlabelled N in the new shoot was used to determine the remobilization of N from storage. Initially, growth was unaffected by N supply. After May, High N enhanced growth for both species but the nature of their growth response differed. For both species, new shoot biomass and leaf number increased but root biomass production was affected for V. myrtillus only. Whole plant biomass production was similar for both species under High N, but was greater for V. vitis-idaea under Low N. The amount of N remobilized to support new shoot growth was similar for the two species and was independent of N current supply. N was remobilized predominantly from previous year leaves for V. vitis-idaea and from previous year stems and roots for V. myrtillus. The contribution of remobilization to new shoot N was similar for the two species, but depended on N supply. Remobilization was faster in V. myrtillus, but lasted longer in V. vitis-idaea. The results are discussed in relation to species growth in N-poor environments, focusing on the extent to which species-differences in the dynamic of N remobilization and growth may explain their adaptation to constant and/or changeable N supply.

Magnoliopsida↗
PubMed2000

Exclusion of grass roots from soil organic layers by Calluna: the role of ericoid mycorrhizas.

The role of ericoid mycorrhizal colonization in competition between the dwarf shrub Calluna vulgaris and coarse grass Nardus stricta was investigated. Nardus was grown alone, or in competition with Calluna, in a layered organic/sand substrate with and without inoculation with the ericoid mycorrhizal endophyte Hymenoscyphus ericae, and with and without the addition of nitrogen. Root length and allocation between different substrate layers was assessed along with plant biomass, nutrient uptake and mycorrhizal colonization. Calluna was the superior competitor for nutrients, probably because of its ability to concentrate root growth in the upper organic layer. In the presence of Calluna both the absolute amount and proportion of Nardus root length in the organic layer were reduced, and this reduction was greatest when Calluna was mycorrhizal. The presence of ericoid mycorrhizal colonization did not reduce Nardus shoot nutrient content or concentration, suggesting that ericoid mycorrhizal suppression of Nardus growth was not due to nutrient competition: alternative mechanisms of interference are discussed.

Ecology↗
PubMed1997

Subtalar arthrodesis with interposition tricortical iliac crest graft for late pain and deformity after calcaneus fracture.

We are reporting our experience using tricortical interposition iliac crest grafting in the management of late pain and deformity after calcaneus fracture. Ten patients underwent this procedure, which was performed by the senior author. All but one were followed up with a questionnaire, physical examination, and repeat x-rays. The technique failed in one severely osteoporotic individual because of the graft sinking into the calcaneus. The experience led to two technique modifications that were evaluated in this study.

Arthrodesis↗
PubMed1997

Stress fracture of the tibia after arthrodesis of the ankle or the hindfoot.

We studied twelve patients who had a stress fracture of the tibia and one patient who had a stress fracture of the fibula after arthrodesis of the ankle or the foot. A second stress fracture subsequently developed in two patients. All but two patients were managed non-operatively, and the fractures healed uneventfully. One patient who was managed operatively had a below-the-knee amputation to treat a painful non-union of a tibial fracture, and the other had interlocking intramedullary nailing for a displaced fracture. All but one of the arthrodesis sites had fused before the stress fracture occurred. All of the stress fractures that occurred after arthrodesis of the ankle were in the middle and distal aspects or the distal aspect of the tibia, while those that occurred after triple arthrodesis were in the distal aspect of the fibula or the medial malleolus. Although six of the thirteen patients still had uncorrected alignment and deformity after the arthrodesis, optimum alignment after the arthrodesis did not preclude the occurrence of a stress fracture. We conclude that stress fracture must be considered in the differential diagnosis of pain months or even years after solid fusion at the site of an ankle or triple arthrodesis.

Adult↗
PubMed1996

Inhibition of chitinolytic activities from tree species and associated fungi.

Effects of two inhibitors, allosamidin and (2-acetamido-2-deoxy-D-glucopyranosylidene)amino phenylcarbamate (PUGNAC), have been assessed on chitinolytic activities of two plants, Pinus sylvestris L. and Eucalyptus pilularis Sm., and of seven fungi. Pinus sylvestris and E. pilularis root endochitinase activities were inhibited by allosamidin. Activities of P. sylvestris were more sensitive to inhibition than those of E. pilularis. The mechanism of inhibition varied with the plant species and the enzyme involved. PUGNAC inhibited beta-N-acetylglucosaminidase and exochitinase activities in root extracts from both plant species. In all cases PUGNAC acted as a reversible competitive inhibitor. Both inhibitors also affected chitinolytic activities from the fungi screened. Allosamidin inhibited endochitinase activities from both the mycorrhizal and pathogenic fungi tested. In addition, exochitinase activity from the ectomycorrhizal fungus Paxillus involutus (Batsch) Fr. was inhibited by allosamidin. PUGNAC inhibited beta-N-acetylglucosaminidase activity from all the fungi tested. PUGNAC was also a potent inhibitor of both exo- and endochitinase activities from the fungi, except P. involutus. Competitive inhibition was the most common form. These findings show allosamidin does inhibit endochitinase activity in plants and the ability of PUGNAC to inhibit not only beta-N-acetylglucosaminidase activity but also fungal endochitinase activity may be useful to distinguish between host and fungal endochitinase activities in symbiotic or pathogenic dual systems.

Acetylglucosamine↗
PubMed1996

Foot function in diabetic patients after partial amputation.

The function of partially amputated feet in 10 patients with diabetes mellitus was studied. First-step bilateral barefoot plantar pressure distribution and three-dimensional kinematic data were collected using a Novel EMED platform and three video cameras. Analysis of the plantar pressure data revealed a significantly greater mean peak plantar pressure in the feet with transmetatarsal amputation (TMA) than in the intact feet of the same patients. The heels of the amputated feet had significantly lower mean peak plantar pressures than all the forefoot regions. A significantly greater maximum dynamic dorsiflexion range of motion was seen in the intact compared with the TMA feet. However, no difference was noted in the static dorsiflexion range of motion between the two feet and there was, therefore, a trend for the TMA feet to use less of the available range of motion. Given the altered kinematics and elevated plantar pressures noted in this study, careful postsurgical footwear management of feet with TMA would appear to be essential if ulceration is to be prevented.

Aged↗
PubMed1995

Late reconstruction of the midfoot and tarsometatarsal region after trauma.

The management of painful arthritis and deformity after trauma to the midfoot starts with careful assessment by physical examination and appropriate investigation to identify the affected joints. Conservative treatment may be very effective and includes the use of NSAIDs, custom insoles with arch support, and a rocker-bottom sole with extended steel shank with or without a SACH heel. If this treatment fails, usually a year after the injury, then arthrodesis of all the symptomatic joints with restoration of the arch and alignment of the weight-bearing surface is the recommended treatment. The long-term results of these fusions may be compromised by the subsequent development of arthritis in adjacent joints.

Arthrodesis↗
PubMed1994

Reliability of standard foot radiographic measurements.

Fifty standing dorsoplantar and lateral foot radiographs were obtained on a consecutive series of patients seen in an orthopaedic foot and ankle clinic. These radiographs were duplicated, and eight common foot measurements were made on each pair by six experienced examiners. Measurements were made in two ways: first by a subjective visual assessment, and second by quantitative evaluation made according to strictly defined criteria. All measurements were made under controlled, ideal conditions with similar high quality goniometers. The results demonstrated overall greater reliability in the quantitative methods than the non-quantitative methods. For each of the quantitative techniques, a cumulated frequency distribution of differences between examiners was calculated. The approximate 95% bounds for these measures were: hallux-metatarsophalangeal angle = 6 degrees, first intermetatarsal angle = 4 degrees, metatarsophalangeal-5 angle = 11 degrees, fourth intermetatarsal angle = 4 degrees, AP talocalcaneal angle = 20 degrees, lateral talocalcaneal angle = 12 degrees, sesamoid station = 2 grades, and forefoot width = 5 mm. Physicians using these parameters to make decisions regarding patient care and clinical outcomes need to keep in mind these potential errors in making foot radiographic measurements.

Ankle↗
PubMed1990

The assessment of dynamic foot-to-ground contact forces and plantar pressure distribution: a review of the evolution of current techniques and clinical applications.

The objective documentation of foot function before and after therapeutic intervention will be greatly enhanced by the utilization of devices capable of measuring dynamic foot pressure distribution. Efforts to develop this technology date back to the late 19th century, but only with recent advances in computers has it been possible to produce quantitatively accurate high resolution foot pressure distribution with high sampling rates and easily interpreted graphic displays. Over the years, a variety of methods have been employed to study foot pressure. Many of these techniques have already improved our understanding of the foot and its function, and have had an impact on the way we practice. Effective clinical utilization of these new investigative tools depends on an understanding of their scientific basis, capabilities and limitations.

Biomedical Engineering↗
PubMed1990

Problematic fractures and dislocations in the foot and ankle of athletes.

Foot fractures can significantly compromise an athlete's career. Early recognition and treatment of occult fractures will reduce lay-off time and decrease the likelihood of prolonged impairment of performance. The appropriate treatment of radiographically obvious fractures will have a similar effect. The key to making an early diagnosis is the recognition of characteristic patterns on physical examination and the aggressive investigation of persistent foot pain in the athlete, whether it follows an injury or not. When a fracture is not apparent on routine radiographs, special diagnostic techniques, particularly technetium bone scanning, can effectively screen for bony injury. In the competitive athlete there is no reason to adopt a "wait-and-see" attitude. The approach in treating these injuries in athletes should be similarly definitive. If continued participation will delay healing or resolution of the symptoms, it should not be tolerated.

Ankle Injuries↗
PubMed1989

Assessment and management of pes cavus in Charcot-Marie-tooth disease.

The sequential approach to evaluating the cavus foot is integrated with a description and assessment of the various treatment options. Decision making in the treatment of these cases is complicated by the progressive neurologic condition that underlies many of these deformities. An effort is made to recommend the most appropriate surgical intervention based on the nature of the deformity and its rigidity. Although these principles apply to all cavus feet, the deformity in Charcot-Marie-Tooth disease is the most difficult to treat and the most prone to recurrence because of the progressive nature of the muscular imbalance causing it.

Charcot-Marie-Tooth Disease↗
PubMed1987

Magnetic resonance imaging in the diagnosis of disruption of the posterior tibial tendon.

Magnetic resonance imaging (MRI), a useful technique of studying soft tissues of the body, can be very effective in assessing the integrity of tendons. Usually a patient with a complete tear of the posterior tibial tendon has characteristic physical findings. In the patient presented, MRI demonstrated a complete disruption of the posterior tibial tendon, despite the absence of the commonly associated clinical findings. In view of the difficulties encountered with attempted tenography of the completely torn posterior tibial tendon, MRI provides a sensitive alternative diagnostic technique.

Adult↗