Probing the magnetic moment of FePt micromagnets prepared by Focused Ion Beam milling

We investigate the degradation of the magnetic moment of a 300 nm thick FePt film induced by Focused Ion Beam (FIB) milling. A $1~\mu \mathrm{m} \times 8~\mu \mathrm{m}$ rod is milled out of a film by a FIB process and is attached to a cantilever by electron beam induced deposition. Its magnetic moment is determined by frequency-shift cantilever magnetometry. We find that the magnetic moment of the rod is $\mu = 1.1 \pm 0.1 \times 10 ^{-12} \mathrm{Am}^2$, which implies that 70% of the magnetic moment is preserved during the FIB milling process. This result has important implications for atom trapping and magnetic resonance force microscopy (MRFM), that are addressed in this paper.Comment: 4 pages, 4 figure

Global assessment of nitrogen deposition effects on terrestrial plant diversity : a synthesis

Atmospheric nitrogen (N) deposition is it recognized threat to plant diversity ill temperate and northern parts of Europe and North America. This paper assesses evidence from field experiments for N deposition effects and thresholds for terrestrial plant diversity protection across a latitudinal range of main categories of ecosystems. from arctic and boreal systems to tropical forests. Current thinking on the mechanisms of N deposition effects on plant diversity, the global distribution of G200 ecoregions, and current and future (2030) estimates of atmospheric N-deposition rates are then used to identify the risks to plant diversity in all major ecosystem types now and in the future. This synthesis paper clearly shows that N accumulation is the main driver of changes to species composition across the whole range of different ecosystem types by driving the competitive interactions that lead to composition change and/or making conditions unfavorable for some species. Other effects such its direct toxicity of nitrogen gases and aerosols long-term negative effects of increased ammonium and ammonia availability, soil-mediated effects of acidification, and secondary stress and disturbance are more ecosystem, and site-specific and often play a supporting role. N deposition effects in mediterranean ecosystems have now been identified, leading to a first estimate of an effect threshold. Importantly, ecosystems thought of as not N limited, such as tropical and subtropical systems, may be more vulnerable in the regeneration phase. in situations where heterogeneity in N availability is reduced by atmospheric N deposition, on sandy soils, or in montane areas. Critical loads are effect thresholds for N deposition. and the critical load concept has helped European governments make progress toward reducing N loads on sensitive ecosystems. More needs to be done in Europe and North America. especially for the more sensitive ecosystem types. including several ecosystems of high conservation importance. The results of this assessment Show that the Vulnerable regions outside Europe and North America which have not received enough attention are ecoregions in eastern and Southern Asia (China, India), an important part of the mediterranean ecoregion (California, southern Europe). and in the coming decades several subtropical and tropical parts of Latin America and Africa. Reductions in plant diversity by increased atmospheric N deposition may be more widespread than first thought, and more targeted Studies are required in low background areas, especially in the G200 ecoregions

The impact of hunting on tropical mammal and bird populations

Hunting is a major driver of biodiversity loss, but a systematic large-scale estimate of hunting-induced defaunation is lacking. We synthesized 176 studies to quantify hunting-induced declines of mammal and bird populations across the tropics. Bird and mammal abundances declined by 58% (25 to 76%) and by 83% (72 to 90%) in hunted compared with unhunted areas. Bird and mammal populations were depleted within 7 and 40 kilometers from hunters’ access points (roads and settlements). Additionally, hunting pressure was higher in areas with better accessibility to major towns where wild meat could be traded. Mammal population densities were lower outside protected areas, particularly because of commercial hunting. Strategies to sustainably manage wild meat hunting in both protected and unprotected tropical ecosystems are urgently needed to avoid further defaunation

Polarization tomography of metallic nanohole arrays

We report polarization tomography experiments on metallic nanohole arrays with square and hexagonal symmetry. As a main result, we find that a fully polarized input beam is partly depolarized after transmission through a nanohole array. This loss of polarization coherence is found to be anisotropic, i.e. it depends on the polarization state of the input beam. The depolarization is ascribed to a combination of two factors: i) the nonlocal response of the array due to surface plasmon propagation, ii) the non-plane wave nature of a practical input beam.Comment: 4 pages, 3 figures, 1 table, submitted to PR

Anthracnose in white lupin : genetic diversity, virulence and host resistance

White lupin (Lupinus albus L.) is a grain legume that is known for its high protein content, nutritional quality, efficient nitrogen fixation and unique ability to form specialized cluster roots that support phosphorus uptake. Despite a severe production decline at the end of the past century, white lupin has seen a recent revival to sustain the demand for plant-based protein and reduce Europes dependency on imported soybean. A major problem in (white) lupin cultivation is anthracnose disease, caused by the globally dispersed, seed- and air-borne fungal pathogen Colletotrichum lupini. This PhD thesis aims to provide insights on how to sustainably control anthracnose disease in white lupin in order to support its re-introduction into European cultivation systems. It describes (i) the genetic diversity, phylogeography and virulence of C. lupini, (ii) the development of a high-throughput phenotyping protocol to reliably screen white lupin germplasm, (iii) a genome-wide association study identifying resistance candidate genes and (iv) the exploration of effective seed treatments to reduce the primary pathogen inoculum. Multi-locus phylogeny and morphological characterization of 39 C. lupini isolates showed that diversity is greater than previously reported, distinguishing a total of six genetic groups and ten distinct morphotypes. Highest diversity was found across the South American Andes, indicating it to be the center of origin of C. lupini. Results reveal that the current pandemic is caused by strains belonging to genetic group II, which are spread globally, and are genetically and morphologically uniform. Group II isolates were shown to be highly aggressive on tested white and Andean lupin accessions. Isolates belonging to the other five genetic groups were mostly found locally and showed distinct virulence patterns on both white and Andean lupin accessions. Despite its uniformity, it was shown that two highly virulent group II isolates from Chile could overcome resistance of elite white lupin breeding material, stressing the need to implement phytosanitary protocols for international seed transports. A reliable high-throughput phenotyping tool was developed to identify anthracnose resistance in white lupin germplasm and study pathogen-host interactions. Phenotyping under controlled conditions, performing stem wound inoculation on seedlings, showed to be applicable for high-throughput and its disease scores strongly correlated with two-year Swiss field disease assessments (r = 0.95) and yield (r = -0.64). Phenotyping a diverse set of 40 white lupin accessions revealed eight accessions with improved resistance to anthracnose, which can be incorporated into white lupin breeding programs. A genome-wide association study (GWAS) was done to dissect the genetic architecture for anthracnose resistance in white lupin. White lupin genotypes, collected from the center of domestication and traditional cultivation regions, were screened for anthracnose resistance and characterized through genotyping-by-sequencing (GBS). GWAS revealed two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161, encoding a RING zinc-finger E3 ubiquitin ligase potentially involved in plant immunity. Further validation experiments are now required to confirm involvement in plant resistance. Population analysis showed a remarkably fast linkage disequilibrium (LD) decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarce breeding efforts in white lupin. A total of eleven different seed treatments was tested in field trials in Switzerland between 2018 and 2021 to identify treatments that reduce C. lupini infection levels in white lupin. Treatments consisted of hot water, steam, electron, long term storage, vinegar, plant extracts and biological control agents (BCAs). The BCAs were tested under controlled conditions for potential antagonistic activity against C. lupini during white lupin infection prior to field trials. Results showed that long term storage and vinegar treatments can successfully reduce disease incidence and increase yield to levels similar to those observed for certified seeds. In order to sustainably and effectively control anthracnose disease in white lupin, an integrative approach, including modern breeding efforts, disease prevention strategies and mixed cropping systems, is recommended. Further research is required to increase our understanding on white lupin-C. lupini interaction and to identify genetic regions involved in resistance or virulence, respectively, which could greatly support white lupin breeding. This thesis provides the basis to further explore C. lupini population dynamics, virulence and host-speciation, white lupin resistance mechanisms and sustainable ways to control anthracnose disease in order to further facilitate successful white lupin cultivation.Die Weiße Lupine (Lupinus albus L.) ist eine Körnerleguminose mit hohem Proteingehalt, guter Nährstoffqualität, effizienter Stickstofffixierung und, aufgrund spezialisierter Proteoidwurzeln, erhöhter Phosphoraufnahme. Trotz eines starken Produktionsrückgangs Ende des 20. Jahrhunderts erlebt die Weiße Lupine jüngst einen Aufschwung aufgrund der Nachfrage nach pflanzlichem Eiweiß und Europas Abhängigkeit von Sojaimporten. Ein großes Problem im Anbau der (weißen) Lupine ist die Anthraknose-Krankheit, die durch den weltweit verbreiteten, samen- und luftbürtigen Pilzerreger Colletotrichum lupini verursacht wird. Ziel dieser Dissertation ist es, Erkenntnisse über Bekämpfungsstragien der Lupinenanthraknose zu gewinnen, um die Wiedereinführung dieser Kulturpflanze in europäische Anbausysteme zu unterstützen. Sie beschreibt (i) die genetische Vielfalt und Virulenz von C. lupini, (ii) die Entwicklung eines Hochdurchsatz-Phänotypisierungsprotokolls, (iii) eine genomweite Assoziationsstudie zur Identifizierung von Resistenzgen-Kandidaten und (iv) die Untersuchung wirksamer Saatgutbehandlungen zur Reduzierung des primären Pathogeninokulums. Charakterisierung von 39 C. lupini-Isolaten zeigen dass die Diversität größer ist als bisher berichtet, wobei insgesamt sechs genetische Gruppen und zehn Morphotypen unterschieden werden. Die größte Vielfalt wurde in den südamerikanischen Anden gefunden, was auf das Genzentrum von C. lupini hindeutet. Die Ergebnisse zeigen, dass die aktuelle Pandemie durch weltweit verbreitete und homogene Stämme der genetischen Gruppe II verursacht wird. Isolate der Gruppe II erwiesen sich als äußerst aggressiv gegenüber der Weißen und Anden-Lupine. Isolate der anderen fünf genetischen Gruppen wurden meist lokal gefunden und zeigten sowohl bei der Weißen als auch bei der Anden-Lupine unterschiedliche Virulenzmuster. Trotz ihrer Einheitlichkeit konnte gezeigt werden, dass zwei hochvirulente Isolate der Gruppe II aus Chile die Resistenz von fortgeschrittenem Zuchtmaterial der Weißen Lupine überwinden konnten. Dies unterstreicht die Notwendigkeit der Umsetzung von Pflanzenschutzprotokollen für internationale Saatguttransporte. Es wurde ein zuverlässiges Phänotypisierungsprotokoll mit hohem Durchsatz entwickelt, um Anthraknoseresistenz in genetischen Ressourcen der Weißen Lupine zu identifizieren. Die Phänotypisierung unter kontrollierten Bedingungen und mittels Wundinokulation des Stängels erwies sich als geeignet für den Hochdurchsatz, und die Krankheitsindizes korrelierten stark mit den Krankheitsbonituren (r = 0,95) und dem Ertrag (r = -0,64) eines zweijährigen Parzellenversuchs im Feld. Die Phänotypisierung von 40 Weiße Lupine-Akzessionen ergab acht Akzessionen mit verbesserter Anthraknose-Resistenz. Eine genomweite Assoziationsstudie (GWAS) wurde durchgeführt, um die genetische Architektur der Anthraknoseresistenz bei weißer Lupine zu entschlüsseln. Weiße Lupine Genotypen aus dem Domestikationszentrum und traditionellen Anbauregionen wurden mittels zuvor beschriebenem Phänotypisierungprotokoll auf Anthraknoseresistenz untersucht und mittels genotyping-by-sequencing (GBS) charakterisiert. GWAS ergab zwei signifikante SNPs, die mit Anthraknoseresistenz auf dem Gen Lalb_Chr05_g0216161 assoziiert sind. Dieses Gen kodiert für eine RING-Zink-Finger-E3-Ubiquitin-Ligase kodiert, die möglicherweise an der Pflanzenimmunität beteiligt ist. Die Populationsanalyse zeigte einen bemerkenswert schnellen Zerfall des Kopplungsungleichgewichts (LD), eine schwache Populationsstruktur und eine Gruppierung von kommerziellen Sorten mit Landsorten, was der langsamen Domestikations-geschichte und den geringen Züchtungsbemühungen bei der Weißen Lupine entspricht. Insgesamt elf verschiedene Saatgutbehandlungen wurden zwischen 2018 und 2021 in Schweizer Feldversuchen getestet. Die Behandlungen umfassten Heißwasser, Dampf, Elektronenbestrahlung, Langzeitlagerung, Essig, Pflanzenextrakte und biologische Bekämpfungsmittel (BCAs). Die Feldergebnisse zeigten, dass eine Langzeitlagerung und eine Behandlung mit Essig das Auftreten von Krankheiten erfolgreich reduzieren und den Ertrag auf ein ähnliches Niveau wie bei zertifiziertem Saatgut steigern kann. Zur nachhaltigen und wirksamen Bekämpfung der Anthraknose-Krankheit wird ein integrativer Ansatz empfohlen, der moderne Züchtungs-maßnahmen, Strategien zur Krankheitsvorbeugung und Mischkultur umfasst. Diese Arbeit bildet die Grundlage für die weitere Erforschung der Populationsdynamik von C. lupini, der Virulenz und der Wirtsspeziation, der Resistenzmechanismen der Weißen Lupine und nachhaltiger Möglichkeiten zur Bekämpfung der Anthraknosekrankheit, um den erfolgreichen Anbau der Weißen Lupine weiter zu erleichtern