Drought resistance indices for screening of potato (Solanum tuberosum L.) genotypes

Open Access JournalIn breeding for drought tolerance, availability of precise, cheap and easy to apply selection tool is critical. The aim of the present study was to identify potential screening tools that are useful for selection of drought tolerant genotypes in potato and select drought resistant potato genotypes. The study assessed sixty clones arranged in a 10×6 alpha lattice design with two replicates in a managed stress experiment. Two irrigation treatments were applied: fully watered non-stress and terminal drought, where the irrigation water supply to the crop was withheld after 50 % flowering to induce post-flowering stress. Stress indices were calculated based on tuber yield of genotypes in both stressed and non-stressed conditions. Identification of drought tolerant genotypes based on a single index was less informative as different indices identified different genotypes as drought tolerant. Hence, to determine the most desirable drought tolerant clones rank sum of indices, correlation, and bi-plot display of the principal component analysis was employed. The indices modified stress tolerance index based on non-stressed yield, Men productivity, Geometric mean productivity, Stress tolerance index, Harmonic mean, modified stress tolerance index based on stressed yield and Yield index exhibited strong association with both yield under stressed and non-stressed yield. These indices discriminated drought tolerant genotypes with higher tuber yielding potential both under stress and non-stress conditions. Genotypes CIP-398180.612, CIP-397069.5, and CIP-304371.67 were identified as drought tolerant. These genotypes could be potentially grown both under drought prone and potential environments and these selection attributes could help to develop climate resilient potato varieties

Soluble expression, purification and characterization of the full length IS2 Transposase

<p>Abstract</p> <p>Background</p> <p>The two-step transposition pathway of insertion sequences of the IS<it>3 </it>family, and several other families, involves first the formation of a branched figure-of-eight (F-8) structure by an asymmetric single strand cleavage at one optional donor end and joining to the flanking host DNA near the target end. Its conversion to a double stranded minicircle precedes the second insertional step, where both ends function as donors. In IS<it>2</it>, the left end which lacks donor function in Step I acquires it in Step II. The assembly of two intrinsically different protein-DNA complexes in these F-8 generating elements has been intuitively proposed, but a barrier to testing this hypothesis has been the difficulty of isolating a full length, soluble and active transposase that creates fully formed synaptic complexes <it>in vitro </it>with protein bound to both binding and catalytic domains of the ends. We address here a solution to expressing, purifying and structurally analyzing such a protein.</p> <p>Results</p> <p>A soluble and active IS<it>2 </it>transposase derivative with GFP fused to its C-terminus functions as efficiently as the native protein in <it>in vivo </it>transposition assays. <it>In vitro </it>electrophoretic mobility shift assay data show that the partially purified protein prepared under native conditions binds very efficiently to cognate DNA, utilizing both N- and C-terminal residues. As a precursor to biophysical analyses of these complexes, a fluorescence-based random mutagenesis protocol was developed that enabled a structure-function analysis of the protein with good resolution at the secondary structure level. The results extend previous structure-function work on IS<it>3 </it>family transposases, identifying the binding domain as a three helix H + HTH bundle and explaining the function of an atypical leucine zipper-like motif in IS<it>2</it>. In addition gain- and loss-of-function mutations in the catalytic active site define its role in regional and global binding and identify functional signatures that are common to the three dimensional catalytic core motif of the retroviral integrase superfamily.</p> <p>Conclusions</p> <p>Intractably insoluble transposases, such as the IS<it>2 </it>transposase, prepared by solubilization protocols are often refractory to whole protein structure-function studies. The results described here have validated the use of GFP-tagging and fluorescence-based random mutagenesis in overcoming this limitation at the secondary structure level.</p

Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition

<p>Abstract</p> <p>Background</p> <p>Transposition in IS<it>3</it>, IS<it>30</it>, IS<it>21 </it>and IS<it>256 </it>insertion sequence (IS) families utilizes an unconventional two-step pathway. A figure-of-eight intermediate in Step I, from asymmetric single-strand cleavage and joining reactions, is converted into a double-stranded minicircle whose junction (the abutted left and right ends) is the substrate for symmetrical transesterification attacks on target DNA in Step II, suggesting intrinsically different synaptic complexes (SC) for each step. Transposases of these ISs bind poorly to cognate DNA and comparative biophysical analyses of SC I and SC II have proven elusive. We have prepared a native, soluble, active, GFP-tagged fusion derivative of the IS<it>2 </it>transposase that creates fully formed complexes with single-end and minicircle junction (MCJ) substrates and used these successfully in hydroxyl radical footprinting experiments.</p> <p>Results</p> <p>In IS2, Step I reactions are physically and chemically asymmetric; the left imperfect, inverted repeat (IRL), the exclusive recipient end, lacks donor function. In SC I, different protection patterns of the cleavage domains (CDs) of the right imperfect inverted repeat (IRR; extensive <it>in cis</it>) and IRL (selective <it>in trans</it>) at the single active cognate IRR catalytic center (CC) are related to their donor and recipient functions. In SC II, extensive binding of the IRL CD <it>in trans </it>and of the abutted IRR CD <it>in cis </it>at this CC represents the first phase of the complex. An MCJ substrate precleaved at the 3' end of IRR revealed a temporary transition state with the IRL CD disengaged from the protein. We propose that in SC II, sequential 3' cleavages at the bound abutted CDs trigger a conformational change, allowing the IRL CD to complex to its cognate CC, producing the second phase. Corroborating data from enhanced residues and curvature propensity plots suggest that CD to CD interactions in SC I and SC II require IRL to assume a bent structure, to facilitate binding <it>in trans</it>.</p> <p>Conclusions</p> <p>Different transpososomes are assembled in each step of the IS<it>2 </it>transposition pathway. Recipient versus donor end functions of the IRL CD in SC I and SC II and the conformational change in SC II that produces the phase needed for symmetrical IRL and IRR donor attacks on target DNA highlight the differences.</p

Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts

Cerebral arachnoid cysts (ACs) are one of the most common and poorly understood types of developmental brain lesion. To begin to elucidate AC pathogenesis, we performed an integrated analysis of 617 patient-parent (trio) exomes, 152,898 human brain and mouse meningeal single-cell RNA sequencing transcriptomes and natural language processing data of patient medical records. We found that damaging de novo variants (DNVs) were highly enriched in patients with ACs compared with healthy individuals (P = 1.57 × 10-33). Seven genes harbored an exome-wide significant DNV burden. AC-associated genes were enriched for chromatin modifiers and converged in midgestational transcription networks essential for neural and meningeal development. Unsupervised clustering of patient phenotypes identified four AC subtypes and clinical severity correlated with the presence of a damaging DNV. These data provide insights into the coordinated regulation of brain and meningeal development and implicate epigenomic dysregulation due to DNVs in AC pathogenesis. Our results provide a preliminary indication that, in the appropriate clinical context, ACs may be considered radiographic harbingers of neurodevelopmental pathology warranting genetic testing and neurobehavioral follow-up. These data highlight the utility of a systems-level, multiomics approach to elucidate sporadic structural brain disease

The weakest link: competence and prestige as constraints to referral by isolated nurses in rural Niger

BACKGROUND: For a health district to function referral from health centres to district hospitals is critical. In many developing countries referral systems perform well below expectations. Niger is not an exception in this matter. Beyond obvious problems of cost and access this study shows to what extent the behaviour of the health worker in its interaction with the patient can be a barrier of its own. METHODS: Information was triangulated from three sources in two rural districts in Niger: first, 46 semi-structured interviews with health centre nurses; second, 42 focus group discussions with an average of 12 participants – patients, relatives of patients and others; third, 231 semi-structured interviews with referred patients. RESULTS: Passive patients without 'voice' reinforce authoritarian attitudes of health centre staff. The latter appear reluctant to refer because they see little added value in referral and fear loss of power and prestige. As a result staff communicates poorly and show little eagerness to convince reluctant patients and families to accept referral proposals. CONCLUSIONS: Diminishing referral costs and distance barriers is not enough to correct failing referral systems. There is also a need for investment in district hospitals to make referrals visibly worthwhile and for professional upgrading of the human resources at the first contact level, so as to allow for more effective referral patterns

Monitoring the referral system through benchmarking in rural Niger: an evaluation of the functional relation between health centres and the district hospital

BACKGROUND: The main objective of this study is to establish a benchmark for referral rates in rural Niger so as to allow interpretation of routine referral data to assess the performance of the referral system in Niger. METHODS: Strict and controlled application of existing clinical decision trees in a sample of rural health centres allowed the estimation of the corresponding need for and characteristics of curative referrals in rural Niger. Compliance of referral was monitored as well. Need was matched against actual referral in 11 rural districts. The referral patterns were registered so as to get an idea on the types of pathology referred. RESULTS: The referral rate benchmark was set at 2.5 % of patients consulting at the health centre for curative reasons. Niger's rural districts have a referral rate of less than half this benchmark. Acceptability of referrals is low for the population and is adding to the deficient referral system in Niger. Mortality because of under-referral is highest among young children. CONCLUSION: Referral patterns show that the present programme approach to deliver health care leaves a large amount of unmet need for which only comprehensive first and second line health services can provide a proper answer. On the other hand, the benchmark suggests that well functioning health centres can take care of the vast majority of problems patients present with

Technology generation to dissemination:lessons learned from the tef improvement project

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef\u2014an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa\u2019s recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released