The tricot approach: an agile framework for decentralized on-farm testing supported by citizen science. A retrospective.

Matching crop varieties to their target use context and user preferences is a challenge faced by many plant breeding programs serving smallholder agriculture. Numerous participatory approaches proposed by CGIAR and other research teams over the last four decades have attempted to capture farmers' priorities/preferences and crop variety field performance in representative growing environments through experimental trials with higher external validity. Yet none have overcome the challenges of scalability, data validity and reliability, and difficulties in capturing socio-economic and environmental heterogeneity. Building on the strengths of these attempts, we developed a new data-generation approach, called triadic comparison of technology options (tricot). Tricot is a decentralized experimental approach supported by crowdsourced citizen science. In this article, we review the development, validation, and evolution of the tricot approach, through our own research results and reviewing the literature in which tricot approaches have been successfully applied. The first results indicated that tricot-aggregated farmer-led assessments contained information with adequate validity and that reliability could be achieved with a large sample. Costs were lower than current participatory approaches. Scaling the tricot approach into a large on-farm testing network successfully registered specific climatic effects of crop variety performance in representative growing environments. Tricot's recent application in plant breeding networks in relation to decision-making has (i) advanced plant breeding lines recognizing socio-economic heterogeneity, and (ii) identified consumers' preferences and market demands, generating alternative breeding design priorities. We review lessons learned from tricot applications that have enabled a large scaling effort, which should lead to stronger decision-making in crop improvement and increased use of improved varieties in smallholder agriculture.

Chromium binding Bacillus cereus VITSH1-a promising candidate for heavy metal clean up.

Bacteria survive metal stress by several mechanisms and metal binding is one such mechanism which has been screened in the present study to investigate the survival strategies of metal resistant bacteria. The production of siderophores, a metal chelating agent, was detected by chrome azurol S agar assay. The changes in cell wall studied by analysing the peptidoglycan and teichoic acid content indicated an increase in the cell wall content. Evaluation of morphological and physiological alterations like cell size, granularity analysed by SEM and flow cytometry analysis revealed an increase in cell size and granularity respectively. The transformation of phosphates monitored by 31 P NMR analysis indicated the presence of inorganic phosphate. Based on the cell wall changes and the 31 P NMR analysis, the surface charge of the organism was studied by zeta potential which displayed a difference at pH7.

Identification of Blast Resistance in a Core Collection of Foxtail Millet Germplasm.

Blast, also known as leaf spot, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), is a serious disease affecting both forage and grain production in foxtail millet in India. For the identification of new and diverse sources of blast resistance, a foxtail millet core collection comprising 155 accessions was evaluated against the Patancheru isolate (Fx 57) of M. grisea. In a field screen during 2009 and 2010, 21 accessions were identified with neck and head blast resistance against Fx 57. In a greenhouse screen, 11 of the 155 accessions exhibited seedling leaf blast resistance to the same isolate. Further evaluation of the selected 28 accessions (found resistant to neck and head blast under field conditions during 2009 and 2010 or leaf blast in the greenhouse screen) against four M. grisea isolates (Fx 57, Fx 58, Fx 60, and Fx 62 from Patancheru, Nandyal, Vizianagaram, and Mandya, respectively) led to the identification of 16 accessions with leaf, sheath, neck, and head blast resistance to at least one isolate. Two accessions (ISe 1181 and ISe 1547) were free from head blast infection and showed resistance to leaf (score ≤3.0 on a 1-to-9 scale), neck, and sheath blast (score ≤2.0 on a 1-to-5 scale) against all four isolates. In addition, ISe 1067 and ISe 1575 also exhibited high levels of blast resistance. Blast-resistant accessions with superior agronomic and nutritional quality traits can be evaluated in multilocation yield trials before releasing them for cultivation to farmers.

Resistance to Foliar Diseases in a Mini-Core Collection of Sorghum Germplasm.

Anthracnose, leaf blight, and rust are important biotic constraints to grain and forage sorghum production worldwide and are best managed through host plant resistance. A sorghum mini-core collection, consisting of 242 germplasm accessions developed from a core collection of 2,246 landrace accessions originating from 58 countries, was evaluated to identify sources of resistance to foliar diseases. The mini-core accessions were evaluated in anthracnose- and leaf-blight-screening nurseries under artificial inoculation in the rainy and late rainy seasons, respectively, during 2009 and 2010. For rust resistance, screening was done under artificial inoculation in the greenhouse as well as in the field under natural infection. In all, 13 accessions were found resistant (score ≤3.0 on a 1-to-9 scale) to anthracnose and 27 to leaf blight in both 2009 and 2010. Six accessions exhibited resistance to rust in both the greenhouse and the field. In the resistant accessions, a wide range of diversity was observed for agronomic traits such as days to 50% flowering, plant height, and grain yield/plant, and morphological characteristics such as grain or glume color, glume coverage, endosperm texture, and panicle type (ear head compactness). Three mini-core accessions (IS 473, IS 23684, and IS 23521) exhibited resistance to all three diseases. These accessions with multiple disease resistance will be useful in sorghum disease resistance breeding programs.

Prolonged cardiac allograft survival using iodine 131 after human sodium iodide symporter gene transfer in a rat model.

BACKGROUND: Radioiodine is efficiently concentrated by tissues expressing the human sodium iodide symporter (hNIS). OBJECTIVE: To analyze the effects of iodine 131 on acute cardiac allograft rejection after ex vivo hNIS gene transfer in a rat model of cardiac allotransplantation. MATERIALS AND METHODS: Hearts from Brown Norway rats were perfused ex vivo either with UW (University of Wisconsin) solution (n = 9) or UW solution containing 1 x 10(9) pfu/mL of adenovirus 5 plus NIS (Ad-NIS) (n = 18). Donor hearts were transplanted heterotopically into the abdomen of Lewis rats, and recipients were treated on postoperative day 3 with either 15,000 microCi of (131)I or saline solution. The hearts were explanted when no longer beating, and were evaluated histologically for evidence of rejection and other changes. RESULTS: Grafts perfused with the Ad-NIS vector survived significantly longer in recipients injected with (131)I (mean [SD], 11.3 [1.9] days) compared with control animals not treated with (131)I (5.7 [0.65] days) (P < .001). Treatment with (131)I did not prolong graft survival in recipients of hearts that were not perfused with Ad-NIS (5.5 [1.0] vs 5.3 [0.8] days). In Ad-NIS (131)I-treated transplants, the level of myocardial damage on day 6 after surgery, when control hearts were rejected, was significantly lower (60.8 [28.0] vs 99.7 [0.8]; P < .05). CONCLUSION: Our findings indicate that (131)I, after NIS gene transfer, can effectively prolong cardiac allograft survival. To our knowledge, this is the first report of the use of NIS-targeted (131)I therapy in cardiac transplantation. Further studies are required to determine the mechanism of this effect and its potential for clinical application.

Resistance to Grain Mold and Downy Mildew in a Mini-Core Collection of Sorghum Germplasm.

Grain mold and downy mildew are important biotic constraints to grain sorghum (Sorghum bicolor) production worldwide and are best managed through host plant resistance. A sorghum mini-core collection composed of 242 germplasm accessions developed from a core collection of 2,246 landrace accessions from 58 countries was evaluated to identify sources of grain mold and downy mildew resistance. Of the 242 accessions, 140 that flowered during the rainy season (the other 102 accessions were photoperiod sensitive) were screened for grain mold resistance in a grain mold nursery under field epiphytotic conditions during 2007 and 2008. All 242 accessions were screened for downy mildew in the greenhouse using a sandwich inoculation technique. Fifty accessions were resistant to grain mold (≤10% mean severity). These resistant accessions represented four basic and six intermediate races of sorghum that originated from 21 countries and exhibited considerable diversity for agronomic and morphological traits. Downy mildew resistance (mean incidence ≤10%) was observed only in six (IS 28747, IS 31714, IS 23992, IS 27697, IS 28449, and IS 30400) of the 242 accessions. One accession, IS 23992, exhibited resistance to both the diseases. The morphologically and agronomically diverse accessions that are resistant to grain mold or downy mildew should be useful to sorghum disease resistance breeding programs.

Nitric oxide and TNF-alpha trigger colonic inflammation and carcinogenesis in Helicobacter hepaticus-infected, Rag2-deficient mice.

Recombinase-activating gene-2-deficient (Rag2(-/-)) mice lacking functional lymphocytes provide a useful model of chronic inflammatory bowel disease-emulating events in human colon cancer. Infection of Rag2(-/-) mice with Helicobacter hepaticus led to accumulation of macrophages and neutrophils in the colon, a process temporally related to up-regulation of tissue inducible nitric oxide synthase (iNOS) expression at the site of infection and increased nitric oxide (NO) production, as evidenced by urinary excretion of nitrate. Progressive development of increasingly severe inflammation, hyperplasia, dysplasia, and cancer accompanied these changes. Concurrent administration of an iNOS inhibitor prevented NO production and abrogated epithelial pathology and inhibited the onset of cancer. The presence of Gr-1(+) neutrophils and elevated tumor necrosis factor-alpha (TNF-alpha) expression in colon were required for increased iNOS expression and cancer, whereas interleukin-10 (IL-10) down-regulated TNF-alpha and iNOS expression and suppressed cancer. Anti-inflammatory CD4(+) regulatory lymphocytes also down-regulated iNOS and reduced cancer formation. Collectively, these results confirm essential roles for inflammation, increased TNF-alpha expression, and elevated NO production in colon carcinogenesis.

Dependence of lymphopenia-induced T cell proliferation on the abundance of peptide/ MHC epitopes and strength of their interaction with T cell receptors.

Factors that affect naive T cell proliferation in syngeneic lymphopenic hosts were investigated. 2C T cell receptor (TCR) transgenic T cells lacking both CD8 and CD4 survived but hardly proliferated. Proliferation of CD8(+) 2C cells was proportional to the abundance of cognate peptide/MHC complexes and was severely inhibited by injection of anti-CD8 antibody. Weakly reactive self-peptides slightly enhanced CD8(+) 2C cell proliferation whereas a potent agonist peptide promoted much more rapid proliferation, but inflammation-stimulating adjuvant had only a small effect on the rate of cell proliferation. The findings suggest that under uniform lymphopenic conditions, the widely different rates of proliferation of T cells expressing various TCR, or the same TCR in the presence or absence of CD8, reflect the strength of interaction between TCR and MHC associated with particular self-peptides.

Genetic Resistance of Pearl Millet Male-Sterile Lines to Diverse Indian Pathotypes of Sclerospora graminicola.

Single-cross F1 hybrid cultivars based on cytoplasmic-nuclear male-sterility (CMS) system have contributed significantly to increasing productivity of pearl millet (Pennisetum glaucum). Genetic resistance to downy mildew (Sclerospora graminicola) in parental lines is critical for successful commercial cultivation of a hybrid cultivar. In this study, 46 genetically diverse male-sterile lines (A-lines), including 42 test A-lines, four control A-lines, a commercial hybrid, and a highly susceptible line, were evaluated in disease nurseries at four diverse locations in India and compared with pathotype isolates from the same locations under greenhouse environments. Variability in downy mildew incidence (0 to 100%) due to genetic differences among lines, among pathotypes, and that due to line × pathotype interaction were all highly significant (P < 0.001). In the field experiment, eight of the 42 test A-lines, including 841A (control), that recorded ≤10% disease incidence, were identified as resistant compared with 84 to 100% incidence on the control susceptible line 7042S. Resistance in eight of these test A-lines (863A, ICMA 88004, -94333, -98222, -98111, -92777, and -96666) and 841A was confirmed against the four pathotypes in greenhouse experiments. Cluster analysis of downy mildew incidence data from field and greenhouse experiments, using the Euclidian distance, classified the 48 lines into four distinct groups with the above eight A-lines in the resistant group. These resistant A-lines would be useful in the development of F1 hybrids with stable resistance to diverse pathotypes of downy mildew in India.

Homeostasis-stimulated proliferation drives naive T cells to differentiate directly into memory T cells.

The developmental requirements for immunological memory, a central feature of adaptive immune responses, is largely obscure. We show that as naive CD8 T cells undergo homeostasis-driven proliferation in lymphopenic mice in the absence of overt antigenic stimulation, they progressively acquire phenotypic and functional characteristics of antigen-induced memory CD8 T cells. Thus, the homeostasis-induced memory CD8 T cells express typical memory cell markers, lyse target cells directly in vitro and in vivo, respond to lower doses of antigen than naive cells, and secrete interferon gamma faster upon restimulation. Like antigen-induced memory T cell differentiation, the homeostasis-driven process requires T cell proliferation and, initially, the presence of appropriate restricting major histocompatibility complexes, but it differs by occurring without effector cell formation and without requiring interleukin 2 or costimulation via CD28. These findings define repetitive cell division plus T cell receptor ligation as the basic requirements for naive to memory T cell differentiation.

Socio-economic rehabilitation programmes of LEPRA India--methodology, results and application of needs-based socio-economic evaluation.

There is now a better understanding of the scope and process of rehabilitation. The approach recognizes the impact of leprosy on the individual, aims to understand the needs and concerns of those affected, their families and community in the rehabilitation process, and that aims to restore the person to normal social life. LEPRA India has undertaken socio-economic rehabilitation (SER) activities in its projects in Andrah Pradesh and Orissa States in India with a holistic approach that has been evolutionary, developmental and participatory. A SER Officer (SERO) was posted to each project. A plan was formulated by the SERO with participation of all project staff. The main emphasis of the programme was on active participation of the affected person in the rehabilitation process. A needs-assessment study was conducted in the target population using a semi-structured questionnaire. Information was elicited about social and economic status, before and after the disease, and the current rehabilitation needs of the persons affected. The next step was meeting the needs through interventions by the SER staff. The impact of the programme on restoration of social and economic status of the affected persons was analysed. The paper stresses the importance of assessing the needs of persons affected by leprosy, structuring a rehabilitation programme with the active participation of the affected person and evaluating the impact of the interventions in restoring normal social and economic life.

Involvement of epitope mimicry in potentiation but not initiation of autoimmune disease.

We have examined whether the peptide (368-381) from the murine adenovirus type 1 E1B sequence, exhibiting a high degree of homology with the known pathogenic thyroglobulin (Tg) T cell epitope (2695-2706), can induce experimental autoimmune thyroiditis (EAT) in SJL/J mice. The viral peptide was a poor immunogen at the T or B cell level and did not elicit EAT either directly or by adoptive transfer assays. Surprisingly, however, the viral peptide was highly antigenic in vitro, activating a Tg2695-2706-specific T cell clone and reacting with serum IgG from mice primed with the Tg homologue. The viral peptide also induced strong recall responses in Tg2695-2706-primed lymph node cells, and subsequent adoptive transfer of these cells into naive mice led to development of highly significant EAT. These data demonstrate that nonimmunogenic viral peptides can act as agonists for preactivated autoreactive T cells and suggest that epitope mimicry may at times play a potentiating rather than a precipitating role in the pathogenesis of autoimmune disease.

Virulence Characterization of Single-Zoospore Isolates of Sclerospora graminicola from Pearl Millet.

Sclerospora graminicola, the causal agent of downy mildew in pearl millet, is well-known for variation in its virulence pattern. Nine single-zoospore isolates (Sg 026-Z-1 to Sg 026-Z-9) derived from an oosporic isolate Sg 026 from a pearl millet F1 hybrid cultivar Nath 4209 grown in a farmer's field in a village, Veelad, in Maharashtra state, India, and three controls (Sg 026, Field-1, and Field-2) were evaluated for their virulence in two experimental runs in a greenhouse. The isolates were maintained on pot-grown seedlings of a highly susceptible pearl millet line, 7042S, in a greenhouse through asexual (sporangial) generations. Pot-grown seedlings of six pearl millet potential differential lines/cultivars (7042S, NHB 3, MBH 110, ICMH 451, 843B, and 852B) were spray-inoculated with a sporangial suspension (5 × 105 sporangia ml-1) and maintained in a greenhouse at 25 ± 2°C. Data were recorded for latent period (days) and disease incidence (%), from which a virulence index (incidence × latent period-1) was calculated to quantify disease-causing potential of isolates. Results indicated significant variation in latent period, incidence, and virulence index among isolates. The isolates were classified into four distinct pathotype groups based on their virulence indices on six pearl millet lines. Because of the significant variation for virulence in the S. graminicola population infecting Nath 4209, it is recommended that the hybrid be regularly monitored for downy mildew infection in farmers' fields, and be replaced by a resistant cultivar that is genetically unrelated to the parental lines of Nath 4209. This will help delay or avoid development of downy mildew epidemics and the resulting heavy loss to pearl millet farmers in the region.

Recruitment of multiple V beta genes in the TCR repertoire against a single pathogenic thyroglobulin epitope.

In autoimmune thyroid disease, the question whether thyroid-infiltrating, autoreactive T cells are derived from a polyclonal or oligoclonal subset has been the subject of considerable debate. In this report, we have examined the T-cell receptor (TCR) V beta profile of mouse clonal T cells responding to a single thyroiditogenic epitope, the As-restricted, 9mer mouse thyroglobulin (MTg) peptide (2496-04). In vitro recall assays based on lymph node cell (LNC) proliferation and cytokine release demonstrated that this peptide is a minimal T-cell epitope inducing a T-helper 1 (Th1) type of response in SJL hosts. A panel of cloned, interleukin-2 (IL-2)-secreting hybridomas was generated from this Th1 subset and their TCR-V beta gene utilization was assessed by reverse transcription-polymerase chain reaction (RT-PCR). Ten clones derived from two independent fusions were found to utilize three V beta gene families (V beta 2, 4, and 17). To the extent that Tg or other thyroid autoantigens encompass multiple pathogenic epitopes it appears unlikely from these data that a restricted TCR-V beta chain usage will be a general characteristic of thyroiditogenic T cells.

Searching for pathogenic epitopes in thyroglobulin: parameters and caveats.

Last year marked the 40th anniversary of the discovery that thyroglobulin (Tg) is a major autoantigen in autoimmune thyroiditis. The Tg molecule presents unique challenges for epitope mapping owing to its large size and extensive iodination. Consequently, pathogenic determinants have only recently been identified. Here, George Carayanniotis and Varada Rao summarize the approaches used to determine pathogenic Tg T-cell epitopes and discuss caveats in this unusual quest.

Contrasting immunopathogenic properties of highly homologous peptides from rat and human thyroglobulin.

The current lack of amino acid sequence data for mouse thyroglobulin (Tg) necessitates mapping of pathogenic T-cell epitopes on heterologous Tg in mouse experimental autoimmune thyroiditis (EAT). A prevailing assumption has been that epitopes sharing a high degree of amino acid homology among heterologous Tg are likely to exhibit the same immunopathogenic properties in the same host. In this report, we have examined this concept while working with the 18-mer rat(r)Tg(2695-13) peptide that was previously shown to elicit 'A'-restricted T cells and EAT in SJL mice. A major immunopathogenic T-cell epitope was localized within the 12-mer rTg(2695-06). It was found that the human 12-mer homologue that carries two Ser substitutions at Glu2703 and Thr2704 exhibited contrasting properties: it failed to activate Th1 cells in lymphokine and proliferation assays; it did not cross-react with rTg(2695-06) at the T-cell level; and it induced only focal thyroiditis following adoptive transfer of specific lymph node cells. These data highlight the caveat involved in extrapolating results of pathogenic T-cell epitope mapping across heterologous Tgs, even when such epitopes share a high degree of amino acid homology.

Mapping of thyroglobulin epitopes: presentation of a 9mer pathogenic peptide by different mouse MHC class II isotypes.

We have previously reported that the 17mer thyroglobulin (Tg) peptide TgP1 (a.a. 2495-2511) induces experimental autoimmune thyroiditis (EAT) in H-2k mice, a process requiring expression of Ek genes, and in H-2s mice that lack functional E molecules. To test whether this apparent discrepancy was due to recognition of distinct TgP1 determinants in each strain, we mapped in this study minimal T-cell epitopes within TgP1 and examined their pathogenicity in C3H (H-2k) or SJL (H-2s) mice. Truncation analysis using TgP1-specific, CD4+ hybridomas from C3H mice identified two overlapping determinants, (2496-2504) and (2499-2507), that were restricted by the Ek and Ak molecules, respectively. Subsequent challenge of C3H and SJL mice with these 9mer peptides revealed that the Ek-restricted (2496-2504) determinant elicited EAT and specific proliferative LNC responses in both strains, suggesting recognition in the context of As, since this is the only class II molecule expressed in SJL mice. This was further confirmed by blocking of the proliferative LNC response by an As-specific monoclonal antibody. In contrast, the Ak-restricted (2499-2507) determinant induced weak EAT and no proliferative LNC responses in either strain. These data 1) delineate the 9mer (2496-2504) peptide as a minimal Tg T-cell epitope with direct pathogenic potential in mice and 2) highlight the use of nonisotypic MHC class II molecules for the presentation of this peptide in mice of different H-2 haplotypes. T-cell level. Despite its nondominant nature, TgP1 induces experimental autoimmune thyroiditis (EAT) with a genetic pattern similar to that obtained with intact Tg, and elicits strong specific T-cell responses as well as IgG responses that cross-react with Tgs from different species (Chronopoulou et al. 1992). For these reasons, TgP1-mediated EAT provides an excellent model for studying the immunoregulatory mechanisms leading to mononuclear infiltration of the thyroid and hypothyroidism--the main symptoms of Hashimoto's disease in humans (Weetman 1992). Earlier work (Chronopoulou et al. 1993) has demonstrated that Ek expression is a necessary but not sufficient requirement for EAT induction with TgP1 and suggested involvement of the Kk and/or Ak loci in the disease process. In apparent contrast to these findings, however, SJL mice that lack H-2E molecules were found to be EAT-susceptible after TgP1 challenge (Chronopoulou et al. 1992).(ABSTRACT TRUNCATED AT 400 WORDS)

Distinct genetic pattern of mouse susceptibility to thyroiditis induced by a novel thyroglobulin peptide.

Experimental autoimmune thyroiditis (EAT), induced by thyroglobulin (Tg) and adjuvant, is major histocompatibility complex-controlled and dependent on Tg-reactive T cells, but the immunopathogenic T-cell epitopes on Tg remain mostly undefined. We report here the thyroiditogenicity of a novel rat Tg peptide (TgP2; corresponding to human Tg amino acids 2695-2713), identified by algorithms as a site of putative T-cell epitope(s). TgP2 causes EAT in SJL (H-2s) but not in C3H or B10.BR (H-2k), BALB/c (H-2d), and B10 (H-2b) mice. This reveals a new genetic pattern of EAT susceptibility, since H-2k mice are known to be high responders (susceptible) after Tg challenge. Following in vivo priming with TgP2, T cells from only SJL mice proliferated significantly and consistently to TgP2 in vitro, whereas TgP2-specific IgG was observed in all strains tested. Adoptive transfer of TgP2-primed SJL lymph node cells to naive syngeneic recipients induced a pronounced mononuclear infiltration of the thyroid, which was more extensive than that observed after direct peptide challenge. TgP2 is non-immunodominant, since priming of SJL mice with rTg did not consistently elicit T-cell responses to TgP2 in vitro and a TgP2-specific T-cell hybridoma did not respond to antigen presenting cells pulsed with rTg. The data support the notion that Tg epitopes need not be either iodinated or immunodominant in order to cause severe thyroiditis and that the genetic pattern of the disease they induce can be distinct from that of Tg-mediated EAT.

Subcortical hyperintensities on brain magnetic resonance imaging: a comparison between late age onset and early onset elderly depressed subjects.

Subcortical structural changes have been reported to occur in some elderly subjects with late age onset depression. Given the association between diseases affecting subcortical structures and affective disorders, this suggests that these structural changes may be involved in the etiology of late age onset depression in some patients. With the advent of Brain Magnetic Resonance Imaging (MRI), "in vivo" analysis of these subcortical structures is now possible. The authors report a higher occurrence of caudate (60% vs. 11%) and large deep white matter hyperintensities (60% vs. 11%) in late age onset elderly depressed subjects compared with early onset elderly depressed subjects. These results suggest that late age onset depression may be mediated by caudate and white matter structural changes in some patients.

Subcortical hyperintensities on brain magnetic resonance imaging: a comparison of normal and bipolar subjects.

Bipolar disorder has been reported to occur frequently in a number of subcortical diseases. This suggests that subcortical structures may be involved in the etiology of bipolar disorder in some patients. With the advent of brain magnetic resonance imaging (MRI), in vivo visualization of the subcortical white and gray matter is now possible, allowing the examination of these structures. The authors report a higher occurrence of deep white matter lesions in bipolar patients (44%) compared with age-matched controls (6%). The neuroanatomic and clinical correlates of these lesions will be discussed, along with their potential pathophysiologic significance.