Genome-wide association mapping of iron homeostasis in the maize association population

BACKGROUND: Iron (Fe) deficiency in plants is the result of low Fe soil availability affecting 30% of cultivated soils worldwide. To improve our understanding on Fe-efficiency this study aimed to (i) evaluate the influence of two different Fe regimes on morphological and physiological trait formation, (ii) identify polymorphisms statistically associated with morphological and physiological traits, and (iii) dissect the correlation between morphological and physiological traits using an association mapping population. RESULTS: The fine-mapping analyses on quantitative trait loci (QTL) confidence intervals of the intermated B73 × Mo17 (IBM) population provided a total of 13 and 2 single nucleotide polymorphisms (SNPs) under limited and adequate Fe regimes, respectively, which were significantly (FDR = 0.05) associated with cytochrome P450 94A1, invertase beta-fructofuranosidase insoluble isoenzyme 6, and a low-temperature-induced 65 kDa protein. The genome-wide association (GWA) analyses under limited and adequate Fe regimes provided in total 18 and 17 significant SNPs, respectively. CONCLUSIONS: Significantly associated SNPs on a genome-wide level under both Fe regimes for the traits leaf necrosis (NEC), root weight (RW), shoot dry weight (SDW), water (H (2)O), and SPAD value of leaf 3 (SP3) were located in genes or recognition sites of transcriptional regulators, which indicates a direct impact on the phenotype. SNPs which were significantly associated on a genome-wide level under both Fe regimes with the traits NEC, RW, SDW, H (2)O, and SP3 might be attractive targets for marker assisted selection as well as interesting objects for future functional analyses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-014-0153-0) contains supplementary material, which is available to authorized users

The genetic basis of natural variation for iron homeostasis in the maize IBM population

BACKGROUND: Iron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis. RESULTS: In hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively. CONCLUSIONS: From the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2’-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK)

The effects of acute and elective cardiac surgery on the anxiety traits of patients with Marfan syndrome

BACKGROUND: Marfan syndrome is a genetic disease, presenting with dysfunction of connective tissues leading to lesions in the cardiovascular and skeletal muscle system. Within these symptoms, the most typical is weakness of the connective tissue in the aorta, manifesting as aortic dilatation (aneurysm). This could, in turn, become annuloaortic ectasia, or life-threatening dissection. As a result, life-saving and preventative cardiac surgical interventions are frequent among Marfan syndrome patients. Aortic aneurysm could turn into annuloaortic ectasia or life-threatening dissection, thus life-saving and preventive cardiac surgical interventions are frequent among patients with Marfan syndrome. We hypothesized that patients with Marfan syndrome have different level of anxiety, depression and satisfaction with life compared to that of the non-clinical patient population. METHODS: Patients diagnosed with Marfan syndrome were divided into 3 groups: those scheduled for prophylactic surgery, those needing acute surgery, and those without need for surgery (n = 9, 19, 17, respectively). To examine the psychological features of the patients, Spielberger's anxiety (STAI) test, Beck's Depression questionnaire (BDI), the Berne Questionnaire of Subjective Well-being, and the Satisfaction with Life scale were applied. RESULTS: A significant difference was found in trait anxiety between healthy individuals and patients with Marfan syndrome after acute life-saving surgery (p 0.1). Finally, a significant, medium size effect was found between patient groups on the Joy in Living scale (F (2.39) = 3.51, p = 0.040, eta2 = 0.15). CONCLUSIONS: Involving psychiatric and mental-health care, in addition to existing surgical treatment interventions, is essential for more successful recovery of patients with Marfan syndrome

Parametricity and Dependent Types

Reynolds' abstraction theorem shows how a typing judgement in System F can be translated into a relational statement (in second order predicate logic) about inhabitants of the type. We (in second order predicate logic) about inhabitants of the type. We obtain a similar result for a single lambda calculus (a pure type system), in which terms, types and their relations are expressed. Working within a single system dispenses with the need for an interpretation layer, allowing for an unusually simple presentation. While the unification puts some constraints on the type system (which we spell out), the result applies to many interesting cases, including dependently-typed ones

Calreticulin mutations affect its chaperone function and perturb the glycoproteome

Calreticulin (CALR) is an endoplasmic reticulum (ER)-retained chaperone that assists glycoproteins in obtaining their structure. CALR mutations occur in patients with myeloproliferative neoplasms (MPNs), and the ER retention of CALR mutants (CALR MUT) is reduced due to a lacking KDEL sequence. Here, we investigate the impact of CALR mutations on protein structure and protein levels in MPNs by subjecting primary patient samples and CALR-mutated cell lines to limited proteolysis-coupled mass spectrometry (LiP-MS). Especially glycoproteins are differentially expressed and undergo profound structural alterations in granulocytes and cell lines with homozygous, but not with heterozygous, CALR mutations. Furthermore, homozygous CALR mutations and loss of CALR equally perturb glycoprotein integrity, suggesting that loss-of-function attributes of mutated CALR chaperones (CALR MUT) lead to glycoprotein maturation defects. Finally, by investigating the misfolding of the CALR glycoprotein client myeloperoxidase (MPO), we provide molecular proof of protein misfolding in the presence of homozygous CALR mutations. Keywords: CP: Cancer; CP: Molecular biology; calreticulin; chaperone; glycoprotein; limited proteolysis-coupled mass spectrometry; myeloperoxidase; myeloproliferative neoplasm; protein folding; proteome

Dem Stickstoff auf der Spur: N2O Prozesse und Nmin Dynamik nach Grünlanderneuerung

Eine weit verbreitete Maßnahme des Grünlandmanagements, die zur Beseitigung von Narbenschäden und zur Steigerung der Futterqualität in unproduktiven Grünländern angewendet wird, ist die Grünlanderneuerung. Die mechanische Bearbeitung von Grünlandböden und die dadurch gesteigerte Mineralisation durch den Abbau organischer Bodensubstanz und der alten Grasnarbe kann zu hohen N-Verlusten in Form des klimarelevanten Treibhausgases Lachgas (N2O) und/oder Nitratauswaschung (NO3-) führen. Bisher gibt es jedoch über die Dauer des beschriebenen Effektes, sowie den Einfluss unterschiedlicher Grünlanderneuerungstechniken nur wenige Informationen. Insbesondere für die nationale Treibhausgasbilanzierung ist es jedoch von Bedeutung, die Prozesse der N2O Umsetzung und ihre Quellen zu kennen und zu erfassen, da sich nur so Maßnahmen zur Emissionsminderung ableiten lassen. Zu diesem Zweck wurde ein Parzellenversuch (2013-2015) auf zwei Standorten (Plaggenesch, Anmoorgley) in der Nähe von Oldenburg (Niedersachsen) mit unterschiedlichen Erneuerungsvarianten etabliert. Als Referenzvarianten dienten: Grünlandumwandlung in Ackerland (Mais) und langjähriges Dauergrünland. Die N2O Flüsse und die Dynamik des mineralischen N (Nmin) wurden über einen Zeitraum von zwei Jahren untersucht. Zusätzlich wurden Nmin Profile (0-90 cm) genutzt, um den N-Verlust über Winter zu quantifizieren und das Risiko einer möglichen NO3- Auswaschung abzuschätzen. Obwohl die N2O Flüsse für einen kurzen Zeitraum (2 Monate) nach der Bearbeitung erhöht waren, konnte kein Jahreseffekt festgestellt werden. Im ersten Winter nach dem Aufbrechen der alten Grasnarbe trat jedoch für den Plaggenesch ein erhöhtes Risiko für NO3- Auswaschung auf. Die Untersuchung der N2O-Produktionswege und der N2O-Reduktion zu N2 (dem Endprodukt der Denitrifikation) erfolgte unter Nutzung stabiler Isotope. Hierzu wurde die 15N-Gasflussmethode im Sommer 2014 angewendet (1). Zusätzlich wurden natürlich vorhandene stabile Isotopensignaturen im bodenbürtigen N2O (δ15NbulkN2O, δ18ON2O und δ15NSPN2O = intramolekulare Verteilung von 15N im N2O Molekül) genutzt, um Quellen der N2O-Bildung im ersten Jahr nach Grünlanderneuerung (2013-2014) zu ermitteln. Auf dem Anmoorgley wurden große N-Verluste durch den Prozess der Denitrifikation bestimmt, wobei N2 die Emissionen dominerte. Für den Plaggenesch konnten generell geringere gasförmige Verluste festgestellt werden

Original Contribution Occupational Exposure to Pesticides and Risk of Non-Hodgkin's Lymphoma

Pesticide exposure may be a risk factor for non-Hodgkin's lymphoma, but it is not certain which types of pesticides are involved. A population-based case-control study was undertaken in 2000-2001 using detailed methods of assessing occupational pesticide exposure. Cases with incident non-Hodgkin's lymphoma in two Australian states (n ¼ 694) and controls (n ¼ 694) were chosen from Australian electoral rolls. Logistic regression was used to estimate the risks of non-Hodgkin's lymphoma associated with exposure to subgroups of pesticides after adjustment for age, sex, ethnic origin, and residence. Approximately 10% of cases and controls had incurred pesticide exposure. Substantial exposure to any pesticide was associated with a trebling of the risk of nonHodgkin's lymphoma (odds ratio ¼ 3.09, 95% confidence interval: 1.42, 6.70). Subjects with substantial exposure to organochlorines, organophosphates, and ''other pesticides'' (all other pesticides excluding herbicides) and herbicides other than phenoxy herbicides had similarly increased risks, although the increase was statistically significant only for ''other pesticides.'' None of the exposure metrics (probability, level, frequency, duration, or years of exposure) were associated with non-Hodgkin's lymphoma. Analyses of the major World Health Organization subtypes of non-Hodgkin's lymphoma suggested a stronger effect for follicular lymphoma. These increases in risk of non-Hodgkin's lymphoma with substantial occupational pesticide exposure are consistent with previous work