Multiple statistical approaches of community fingerprint data reveal bacterial populations associated with general disease suppression arising from the application of different organic field management strategies

Multiple statistical analyses of terminal restriction fragment length polymorphism (T-RFLP) data were used to screen and identify bacterial populations involved in general disease suppression in an organically managed soil. Prior to sampling three different management strategies (i.e. mixed hay (H), tilled fallowing and open-field vegetables production) were used during the transition from conventional to organic farming, with and without compost amendment. The H transition strategy consistently led to the lowest damping-off disease incidence on two different crops in separate greenhouse and field experiments. Bacterial population structure in bulk soil and the rhizosphere of both crops was characterized using T-RFLP analyses of amplified 16S rDNA sequences. First, principal component analysis (PCA) revealed changes in the relative abundance of bacterial terminal restriction fragments (TRF) in response to transition strategy and/or compost amendment in eight different experimental contexts. In each context, a different subset of TRF substantially contributed to the variation along the first two principal components. However, terminal restriction fragment M148 contributed significantly to the observed variation in 6 out of the 8 experiments, and moderately in the remaining 2 experiments. As a second approach, nonparametric analyses of variance revealed that the relative abundance of TRF differed among treatments. While the responsive subsets identified varied somewhat by experimental context, M137, M139 and M141 were more abundant in samples from the H transition strategy in multiple experimental contexts. Subsequent correlation analyses revealed that TRF associated with disease suppressive treatments (i.e. H with and without compost) were frequently negatively correlated with damping-off disease incidence. As a group, these TRF were disproportionately associated with lower disease levels further indicating their role in disease suppression. Interestingly, in silico analysis of the bacterial 16S rDNA sequence database revealed that the TRF identified in this study (e.g. M137, M139, M141, and M148) might correspond to well-characterized genera of bacterial biological control agents.     

Detection of nodavirus in barramundi, Lates calcarifer (Bloch), using recombinant coat protein-based ELISA and RT–PCR

The coat protein encoded by the nodavirus RNA2 gene originally isolated from greasy grouper, Epinephelus tauvina , was cloned, expressed as a recombinant polyhistidine-tailed fusion protein and characterized by immunoblot analysis. The purified recombinant protein was used to develop an indirect enzyme-linked immunosorbent assay (ELISA) to detect body exudate and plasma antibodies against the coat protein in both experimentally infected and commercial barramundi. In addition, the nucleotide sequence was employed to develop a RT–PCR detection assay based on the T4 region. The results showed that the virus could be detected as early as 3 days post-infection by RT–PCR while antibodies against the recombinant coat protein were detectable on day 6 post-infection. Among 112 commercial barramundi samples collected from October 1999 to April 2000, 9% showed positive ELISA results which were further verified by Western blot.     

An indirect enzyme-linked immunosorbent assay for diagnosis of American canine hepatozoonosis.

American canine hepatozoonosis (ACH), caused by Hepatozoon americanum, is an emerging tick-borne disease of dogs. An indirect enzyme-linked immunosorbent assay (ELISA) that should facilitate diagnosis of infection and study of the epidemiology of ACH has been developed using H. americanum sporozoites as antigen. Efficacy of the new test as a diagnostic tool was compared with that of skeletal muscle biopsy, the current gold standard for confirming H. americanum infection. Results show that the test is sensitive (93%) and specific (96%) and that it is as reliable as histopathologic examination of skeletal muscle for detecting infection. The ELISA would be suitable as a routine laboratory test for diagnosis of ACH.     

Bilateral occurrence of granulosa-theca cell tumors in an Arabian mare

An Arabian mare was referred for right granulosa-theca cell tumor (GTCT) evaluation. The mare was presented 4.5 years later for a left GTCT, after successfully conceiving and delivering a normal foal in the interim. The concurrent or nonconcurrent occurrence of bilateral GTCT in mares appears to be rare.     

How a DNA polymerase clamp loader opens a sliding clamp

Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.     

A participatory farming system approach for sustainable broomrape (Orobanche spp.) management in the Near East and North Africa

Broomrapes (Orobanche spp.) are aggressive and damaging parasitic weeds which have a tremendous impact on agriculture in East Africa, the Mediterranean region and the Middle East. Despite the availability of technologies to control broomrapes in economically important crops, Orobanche infestation continues to increase, threatening the livelihoods of millions of farmers. Many of the technologies developed have not been effectively disseminated and there has been little or zero adoption by farmers—who continue to use ineffective management practices that exacerbate the problem. The adaptation and dissemination of appropriate management practices are major priorities in broomrape control. However, such work must take into consideration the specific socio-economic characteristics of individual farming systems. Orobanche is a community threat and effective management requires a community-based integrated management approach. Recognizing the central role of farmers in parasitic weed management, a technical cooperation project (TCP) involving FAO, ICARDA and seven countries in the Near East and North Africa (NENA) region was implemented to improve the dissemination of knowledge and skills by using a farmer field school approach: a form of education that uses experiential learning methods to build farmers’ expertise. This paper reviews conventional Orobanche research and development approaches, and highlights weaknesses in the management of the parasitic weed using these approaches as opposed to participatory approaches. The benefits and challenges of participatory farming system approaches in relation to integrated broomrape management (IBM) are also discussed. Lessons learned from achieving community ownership of, and institutional support for, IBM could be applied to other sectors (e.g. public health) in which there is a need for institutional learning and reform. Recommendations are made that include regional collaboration within the framework of a proposed Near East and North Africa Orobanche Management Network (NENAOMAN).     

Barrier analysis detected genetic discontinuity among Ethiopian barley (Hordeum vulgare L.) landraces due to landscape and human mobility on gene flow

The rate of gene flow is greatly affected by the ability of a species to move from one location to another. In Ethiopia the presence of diverse agro-ecological zones, climatic features, rugged mountains and isolated valleys affected the seed-mediated gene flow among regions. Hence, this study was aimed at investigating and detecting presence of any gene barriers and genetic differentiation among regions. Thus, the study was proposed to test whether the high genetic diversity of barley in Ethiopia was due to a reduced gene flow resulting from geographic barriers and/or effects of human activities. A total of 199 barley landraces collected from 10 different geographic regions and altitudes of Ethiopia were analyzed for 15 molecular markers. A barrier analysis was conducted to identify any geographic areas with pronounced genetic discontinuity between the regions that can be interpreted as barriers to gene flow. The result obtained from analysis of molecular variances indicated high genetic variation within regions rather than between regions. Despite high gene flow among regions, we were able to detect genetic discontinuity due to landscape and human mobility for certain barley growing areas. Hence, it was postulated that these barriers have to be considered in genetic resource sampling strategies.     

Genetic diversity and population structure analysis of isolates of the rice false smut pathogen Ustilaginoidea virens in India

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.     

An unusual source of lead causing poisoning

Extract

Sir,—I recently added two nine-month-old heifers showing typical symptoms of lead poisoning, but when the usual search for the source was found. On my third visit the owner produced a half-chewed tape measure which he remembered having mislaid the day before the oneset of the illness of the heifers. Although not expecting it to be the source of the lead, I examined it and found a residue of silvery threads after the organic matter had been calcined. These threads, when dissolved in nitric acid and tested with a solution of potassium iodide, gave a heavy precipitate of “golden spangles” of lead iodide. The heifers had chewed about two feet of tape, which apparently contained enough lead cause the very severe symptoms. After three weeks, they are now recovering.