Potential of LAMP for detection of plant pathogens

Abstract

Accurate detection of plant pathogens is a crucial step in the process of disease management. Methods based on polymerase chain reaction (PCR) have advantages of sensitivity and specificity that make them valuable tools for pathogen detection, but a number of drawbacks to these methods prevent their use in some circumstances. In particular, the cost and complexity of the thermal cycling equipment required for PCR restricts the use of these methods mainly to centralized facilities. Loop-mediated isothermal amplification (LAMP) is a method for the detection of specific nucleic acid sequences and has the potential to overcome many of the limitations of PCR-based methods. The ability of LAMP to amplify a target nucleic acid sequence under isothermal conditions eliminates the need for thermal cycling equipment, allowing testing to be carried out with minimal equipment (a water bath or heated block). Furthermore, simplified methods for the detection of amplification products facilitate the use of LAMP-based methods in the field or in less well-resourced settings. This paper reviews the reports to date of plant pathogen detection using LAMP; highlights the features that make LAMP well suited to applications such as field testing; and explores some recent advances that point to the broader potential for LAMP-based methods to be used in novel phytodiagnostic solutions.

Determining Prognosis in Patients With Pancreatic Endocrine Neoplasms: Can the WHO Classification System Be Simplified?

Purpose

The WHO classification for well-differentiated pancreatic endocrine neoplasms (PENs) incorporates both stage and grade. This study compares the prognostic value of a simplified staging and grading system with the WHO system in a large single-institution study.

Patients and Methods

A prospective database (1982 to 2005) identified 183 patients who underwent operative treatment for PENs. Tumors were staged (< 2 cm primary, ≥ 2 cm primary, or metastases) and graded (low grade: no necrosis and < two mitoses/50 high-powered fields [HPF]; or intermediate grade: necrosis and/or ≥ two mitoses/50 HPF) with a simplified schema. Influence of stage and grade on recurrence and disease-specific survival (DSS) was determined. Prognostic strength was assessed with the concordance index (CI).

Results

Median age of the 183 patients was 56 years, and 53% were women. Median follow-up time was 44 months (range, 1 to 226 months). Classification identified 28 patients (15%) with WHO 1.1 disease, 74 (41%) with 1.2 disease, and 81 (44%) with 2.0 disease. Classification by stage identified 35 patients (19%) with tumors less than 2 cm, 96 (52%) with tumors ≥ 2 cm, and 52 (29%) with nodal or distant metastases. Tumors were low grade in 102 patients (56%). Earlier stage tumors were more likely to be low grade (< 2 cm, 83%; ≥ 2 cm, 61%; metastases, 28%; P < .001). The WHO classification, tumor stage, and grade were associated with 5-year DSS (P < .001). Tumors ≥ 2 cm or metastases are stratified by grade (5-year DSS rate for low v intermediate grade: ≥ 2 cm, 97% v 80%, respectively; P < .001; metastases, 93% v 62%, respectively; P = .05). The CI was 0.72 for WHO, 0.71 for stage, 0.66 for grade, and 0.76 for stage combined with grade.

Conclusion

Accurate prognostic information can be obtained by combining tumor size and metastases with simple grading information based on necrosis and mitotic rate.

Measurement of Femoral Angles in Four Dog Breeds

OBJECTIVE

To develop a standard method of measurement for femoral angles and report values for normal Labrador Retrievers, Golden Retrievers, German Shepherds, and Rottweilers.

STUDY DESIGN

Retrospective evaluation of canine pelvis and femoral radiographs.

SAMPLE POPULATION

Radiographs of Labrador Retrievers, Golden Retrievers, German Shepherds, and Rottweilers (n=100 for each breed).

METHODS

Anatomic lateral distal and proximal femoral angle, mechanical lateral distal and proximal femoral angle, and femoral angle of inclination were measured from radiographs.

RESULTS

For the 4 breeds (Labrador Retrievers, Golden Retrievers, German Shepherds, and Rottweilers, respectively) anatomic lateral distal femoral angles were 97 degrees , 97 degrees , 94 degrees , and 98 degrees ; mechanical lateral distal femoral angles were 100 degrees , 100 degrees , 97 degrees , and 100 degrees ; anatomic lateral proximal femoral angles were 103 degrees , 98 degrees , 101 degrees , and 96 degrees ; mechanical lateral proximal femoral angles were 100 degrees , 95 degrees , 97 degrees , and 93 degrees ; and inclination angles were 134 degrees , 134 degrees , 132 degrees , and 137 degrees . Labrador Retrievers, Golden Retrievers, and Rottweilers had significantly higher values for both anatomic and mechanical lateral distal femoral angle than German Shepherds. Anatomic and mechanical lateral proximal angles were greatest for Labrador Retrievers and lowest for Rottweilers.

CONCLUSION

Anatomic and mechanical femoral joint angles vary between breeds of dogs.

CLINICAL RELEVANCE

Values for femoral joint angles may be clinically useful for angular limb deformity diagnosis, treatment, and assessment.

An assessment of mother-to-child HIV transmission prevention in 16 pilot antenatal clinics in Jamaica

OBJECTIVES

This study aims to determine the number and age distribution of pregnant women testing positive for HIV at 16 selected clinics in Jamaica between 2001 and 2002; the utilization of therapeutic interventions to minimize the risk of mother-to-child transmission (MTCT) and the current status of the HIV-exposed infants and, finally, the number of children who received testing for detection of HIV and to calculate the incidence of MTCT in these children.

METHODS

A retrospective study was carried out at sixteen pilot clinic sites by examining the patient records for all confirmed HIV-positive pregnant mothers and the resultant infants at these facilities for the period January 2001 to December 2002.

RESULTS

One hundred and twenty-three of 8116 pregnant women newly tested positive during the period January 2001 to December 2002; however, 176 HIV+ women delivered. Fifty-three (30%) knew their HIV status prior to participating in the programme. Sixty-two (1.4%) and 61 (1.6%) tested positive in 2001 and 2002, respectively. One hundred and ten (77%) and 113 (83%) mothers and infants, respectively, received ARV therapy, (92% - nevirapine, 8% - zidovudine). Twenty-three per cent of pregnant women received no ARV Forty-four (25.0%) of the 176 infants had a documented ELISA HIV test before eighteen months of age, none had a PCR test. The health status of 40 (23%) of these children was known: 30 (75%) were alive and well, five of whom did not receive any ARV, one (2.5%) was alive and ill and nine (22.5%) were reported dead, five of whom received ARV; 28.6% of infants who did not receive ARV were reported as either dead or ill compared to 13.8% of those receiving ARV CONCLUSION: Though the majority of pregnant women discovered their HIV status during pregnancy, a significant number got pregnant knowing that they were HIV+. The majority of mothers and infants received ARV but the follow-up and testing of infants was limited. Nevirapine is clearly protective in the prevention of MTCT of HIV and should be made universally accessible. All infants delivered to HIV+ mothers should be identified and tested for HIV.

Tumor hypoxia correlates with metastatic tumor growth of pancreatic cancer in an orthotopic murine model

BACKGROUND

The role of tumor hypoxia has become a major focus in cancer research since it influences both local and systemic tumor growth. Oxygen measurements taken in human pancreatic cancer have shown extremely low oxygen tension. The aim of this study was to develop an orthotopic model for pancreatic cancer that mimics the specific tumor microenvironment and to evaluate the role of tumor oxygenation in local tumor growth and systemic dissemination in this model.

MATERIALS AND METHODS

We used two established human pancreatic cancer cell lines for xenobiotic tumor induction. After subcutaneous tumor formation one small tumor piece was transplanted into the pancreatic parenchyma of mice of the different study groups. Upon orthotopic tumor induction tumor oxygenation was measured with the Eppendorf histograph. Histological evaluation was performed with pimonidazole, an in vivo marker of hypoxia.

RESULTS

The tumor take rate was 100% in this model. Metastatic tumor dissemination occurred within the abdominal cavity, and distant metastasis were observed in the lung parenchyma. Oxygen measurements taken in various abdominal organs and xenograft tumor showed a high variation between different organs and xenografted tumors. Tumor oxygenation correlated well with the metastatic score in this model. Furthermore hypoxia was found both in the tumor center and also at the rim of a growing tumor mass. A high number of hypoxic cells were detectable in metastases located in the lung parenchyma.

CONCLUSION

This study provides experimental evidence that tumor hypoxia influences metastatic disease progression and supports recent assumptions that tumor hypoxia is actively involved in progression of pancreatic cancer. It further demonstrates that tumor hypoxia is not only found in the center of a tumor mass, but also occurs at the invasion front.

Efficacy of IV tissue plasminogen activator in acute stroke: does stroke subtype really matter?

BACKGROUND

The National Institute of Neurological Disorders and Stroke (NINDS) trial reported that stroke subtype (e.g., large-artery atherothrombosis, cardioembolism, and lacunae) does not affect response to IV thrombolytic treatment. However, these conclusions were based upon stroke subtypes determined prior to extensive diagnostic evaluation. Because such initial diagnoses are frequently inaccurate, the efficacy of IV recombinant tissue plasminogen activator (rt-PA) based upon verified specific stroke subtypes remains uncertain.

METHODS

The records of consecutive acute stroke patients treated with IV rt-PA at two regional stroke centers were retrospectively reviewed. The final stroke subtype after complete diagnostic evaluation was determined. The relationship between final stroke subtype and response to thrombolytic therapy was then investigated and compared with the results reported in the NINDS trial.

RESULTS

Ninety consecutive patients were studied. After adjusting for baseline NIH Stroke Scale scores, no significant difference in final outcome based on confirmed stroke mechanism was identified.

CONCLUSIONS

These data are consistent with those of the NINDS trial that reported that the efficacy of IV thrombolysis within the 3-hour time window is similar between different stroke subtypes. Based upon these data, allocating treatment of stroke patients with IV rt-PA based upon presumed stroke mechanism may be unnecessary. Such testing may result in time delays that could compromise the efficacy of treatment.

Prognosis for patients newly admitted to hospital with heart failure: survival trends in 12 220 index admissions in Leicestershire 1993-2001

OBJECTIVE

To examine rates of, prognosis following, and the influences on first hospital admission with heart failure in Leicestershire during 1993-2001.

DESIGN

Historical cohort study using record linked discharge and mortality data.

SETTING

Leicestershire, England.

PATIENTS

12 220 individual patients newly hospitalised with heart failure between 1 April 1993 and 31 March 2001.

MAIN OUTCOME MEASURES

30 day and one year survival, temporal trends in survival, and the influence on prognosis of age, sex, comorbidity, social deprivation, and year of hospital admission.

METHODS AND RESULTS

Between 1993/94 and 2000/01, rates of first hospitalisation increased by 62%, from 29 to 47/10 000 population, confined largely to those aged > 65 years. Rates did not increase after 1998. Median age at presentation increased from 74 years in 1993/94 to 77 years in 2000/01 for men but was unchanged (80 years) for women. Overall one and five year survival was 57% and 27%, respectively. There was a 43-45% increase in risk of death for each decade of age at admission and a 14-17% increase associated with male sex. There was a clear influence on outcome of comorbidity but no influence of social deprivation score. Both one month and one year survival were lower for patients whose first heart failure admission was concomitant with acute myocardial infarction. Between 1993/94 and 2000/01 postdischarge cardiovascular survival improved by 50% (p < 0.001).

CONCLUSIONS

Rates of first hospital admission with heart failure reached a plateau in the late 1990s. Case fatality rates remain high and prognosis poor, in particular for those of increasing age, for men, and for patients with concomitant acute myocardial infarction. However, clear trends to improved survival were seen over this time.

Hydroxamate based inhibitors of adenylyl cyclase. Part 1: the effect of acyclic linkers on P-site binding

The adenylyl cyclases (ACs) are a family of enzymes that are key elements of signal transduction by virtue of their ability to convert ATP to cAMP. The catalytic mechanism of this transformation proceeds through initial binding of ATP to the purine binding site (P-site) followed by metal mediated cyclization with loss of pyrophosphate. Crystallographic analysis of ACs with known inhibitors reveals the presence of two metals in the active site. Presently, nine isoforms of adenylyl cyclase are known and unique isoform combinations are expressed in a tissue specific manner. The development of isoform specific inhibitors of adenylyl cyclase may prove to be a useful strategy toward the design of novel therapeutic agents. In order to develop novel AC inhibitors, we have chosen a design approach utilizing molecules with the adenine ring system joined to a metal-coordinating hydroxamic acid via flexible acyclic linkers. The designed inhibitors were assayed against type V AC with the size and heteroatom content of the linkers varied to probe the interaction of the nucleotide and metal binding sites within the enzyme.

Hydroxamate based inhibitors of adenylyl cyclase. Part 2: the effect of cyclic linkers on P-site binding

The adenylyl cyclases (ACs) are a family of enzymes that are key elements of signal transduction by virtue of their ability to convert ATP to cAMP. The catalytic mechanism of this transformation proceeds through initial binding of ATP to the purine binding site (P-site) followed by metal mediated cyclization with loss of pyrophosphate. Previous work in our group identified novel inhibitors which possess an adenine ring joined to a metal-coordinating hydroxamic acid through flexible linkers. Considering the spatial positioning of the metals with respect to the adenine binding site coupled with potentially favorable entropic factors, conformational restriction of the tether through a stereochemistry based SAR employing a rigid cyclic scaffold was explored.

Thoracoscopic-assisted diaphragmatic hernia repair using a thoracic rib resection

OBJECTIVE

To describe the surgical treatment of a dorsal diaphragmatic hernia in an adult horse using thoracic rib resection aided by thoracoscopy and a flank incision.

STUDY DESIGN

Case report.

ANIMAL POPULATION

One client-owned horse.

RESULTS

A six-year-old Dutch warmblood gelding was admitted for colic-associated colonic incarceration in a diaphragmatic hernia. Seven weeks after the initial colic surgery, the gelding underwent surgery to repair the defect. Thoracoscopy and a flank incision were used to identify the location of the hernia and the subsequent site of rib resection. The stomach was adhered to the edges of the defect, leaving only a small residual hole. Resection of the 14th rib provided excellent exposure of the defect and closure of the remaining hernia.

CONCLUSION AND CLINICAL RELEVANCE

Thoracic rib resection can provide access to diaphragmatic hernias in adult horses. Thoracoscopy or a flank incision, or both, may aid in determining which rib is best resected.

Solid variant of alveolar rhabdomyosarcoma with unbalanced t(2;13) and hypotetraploidy, without MYCN amplification

The histological subtype of alveolar rhabdomyosarcoma (AR) is characterised by the cytogenetic translocation t(2;13)(q35;q14) in approximately 70% of cases, a rearrangement rarely present in the embryonal rhabdomyosarcoma (ER) subtype. The MYCN gene is amplified in some cases of AR. We present a young man with an unusual pattern, namely solid variant of AR with hypotetraploidy and the t(2;13) in an unbalanced form. The MYCN gene was not amplified on FISH, but showed increased copy number, consistent with ploidy.