Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize

Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approaches such as QTL meta-analysis and RNA-seq were deployed in order to help prioritizing candidate genes within the QTL target region. Using a selected group of genotypes, field based root analysis by ‘shovelomics’ enabled to accurately collect RSA information of adult maize plants. Shovelomics combined with software-assisted root imaging analysis proved to be an informative and relatively highly automated phenotyping protocol. A QTL interval mapping was conducted using a segregating population at the seedling stage grown in controlled environment. Results enabled to narrow down the QTL interval and to identify new polymorphic markers for MAS in field experiments. A collection of homozygous recombinant NILs was developed by screening segregating populations with markers flanking qroot-yield-1.06. A first set of lines from this collection was phenotyped based on the adapted shovelomics protocol. QTL analysis based on these data highlighted an interval of 1.3 Mb as completely linked with the target QTL but, a larger safer interval of 4.1 Mb was selected for further investigations. QTL meta-analysis allows to synthetize information on root QTLs and two mQTLs were identified in the qroot-yield-1.06 interval. Trascriptomics analysis based on RNA-seq data of the two contrasting QTL-NILs, confirmed alternative haplotypes at chromosome bin 1.06. qroot-yield-1.06 has now been delimited to a 4.1-Mb interval, and thanks to the availability of additional untested homozygous recombinant NILs, the potentially achievable mapping resolution at qroot-yield-1.06 is c. 50 kb.

Impact of anthropogenic stressors on the population genetics of the common bioindicator Dreissena polymorpha (Pallas, 1771)

Toxicant inputs from agriculture, industry and human settlements have been shown to severely affect freshwater ecosystems. Pollution can lead to changes in population genetic patterns through various genetic and stochastic processes. In my thesis, I investigated the impact of anthropogenic stressors on the population genetics of the zebra mussel Dreissena polymorpha. In order to analyze the genetics of zebra mussel populations, I isolated five new highly polymorphic microsatellite loci. Out of those and other already existing microsatellite markers for this species, I established a robust marker set of six microsatellite loci for D. polymorpha. rnMonitoring the biogeographical background is an important requirement when integrating population genetic measures into ecotoxicological studies. I analyzed the biogeographical background of eleven populations in a section of the River Danube (in Hungary and Croatia) and some of its tributaries, and another population in the River Rhine as genetic outgroup. Moreover, I measured abiotic water parameters at the sampling sites and analyzed if they were correlated with the genetic parameters of the populations. The genetic differentiation was basically consistent with the overall biogeographical history of the populations in the study region. However, the genetic diversity of the populations was not influenced by the geographical distance between the populations, but by the environmental factors oxygen and temperature and also by other unidentified factors. I found strong evidence that genetic adaptation of zebra mussel populations to local habitat conditions had influenced the genetic constitution of the populations. Moreover, by establishing the biogeographical baseline of molecular variance in the study area, I laid the foundation for interpreting population genetic results in ecotoxicological experiments in this region.rnIn a cooperation project with the Department of Zoology of the University of Zagreb, I elaborated an integrated approach in biomonitoring with D. polymorpha by combining the analysis techniques of microsatellite analysis, Comet assay and micronucleus test (MNT). This approach was applied in a case study on freshwater contamination by an effluent of a wastewater treatment plant (WWTP) in the River Drava (Croatia) and a complementary laboratory experiment. I assessed and compared the genetic status of two zebra mussel populations from a contaminated and a reference site. Microsatellite analysis suggested that the contaminated population had undergone a genetic bottleneck, caused by random genetic drift and selection, whereas a bottleneck was not detected in the reference population. The Comet assay did not indicate any difference in DNA damage between the two populations, but MNT revealed that the contaminated population had an increased percentage of micronuclei in hemocytes in comparison to the reference population. The laboratory experiment with mussels exposed to municipal wastewater revealed that mussels from the contaminated site had a lower percentage of tail DNA and a higher percentage of micronuclei than the reference population. These differences between populations were probably caused by an overall decreased fitness of mussels from the contaminated site due to genetic drift and by an enhanced DNA repair mechanism due to adaptation to pollution in the source habitat. Overall, the combination of the three biomarkers provided sufficient information on the impact of both treated and non-treated municipal wastewater on the genetics of zebra mussels at different levels of biological organization.rnIn my thesis, I could show that the newly established marker set of six microsatellite loci provided reliable and informative data for population genetic analyses of D. polymorpha. The adaptation of the analyzed zebra mussel populations to the local conditions of their habitat had a strong influence on their genetic constitution. We found evidence that the different genetic constitutions of two populations had influenced the outcome of our ecotoxicological experiment. Overall, the integrated approach in biomonitoring gave comprehensive information about the impact of both treated and non-treated municipal wastewater on the genetics of zebra mussels at different levels of biological organization and was well practicable in a first case study.

Development of models and methods to simulate peptide-assisted nucleation and growth of calcium-minerals

In den vergangenen Jahren wurden einige bislang unbekannte Phänomene experimentell beobachtet, wie etwa die Existenz unterschiedlicher Prä-Nukleations-Strukturen. Diese haben zu einem neuen Verständnis von Prozessen, die auf molekularer Ebene während der Nukleation und dem Wachstum von Kristallen auftreten, beigetragen. Die Auswirkungen solcher Prä-Nukleations-Strukturen auf den Prozess der Biomineralisation sind noch nicht hinreichend verstanden. Die Mechanismen, mittels derer biomolekulare Modifikatoren, wie Peptide, mit Prä-Nukleations-Strukturen interagieren und somit den Nukleationsprozess von Mineralen beeinflussen könnten, sind vielfältig. Molekulare Simulationen sind zur Analyse der Formation von Prä-Nukleations-Strukturen in Anwesenheit von Modifikatoren gut geeignet. Die vorliegende Arbeit beschreibt einen Ansatz zur Analyse der Interaktion von Peptiden mit den in Lösung befindlichen Bestandteilen der entstehenden Kristalle mit Hilfe von Molekular-Dynamik Simulationen.rnUm informative Simulationen zu ermöglichen, wurde in einem ersten Schritt die Qualität bestehender Kraftfelder im Hinblick auf die Beschreibung von mit Calciumionen interagierenden Oligoglutamaten in wässrigen Lösungen untersucht. Es zeigte sich, dass große Unstimmigkeiten zwischen etablierten Kraftfeldern bestehen, und dass keines der untersuchten Kraftfelder eine realistische Beschreibung der Ionen-Paarung dieser komplexen Ionen widerspiegelte. Daher wurde eine Strategie zur Optimierung bestehender biomolekularer Kraftfelder in dieser Hinsicht entwickelt. Relativ geringe Veränderungen der auf die Ionen–Peptid van-der-Waals-Wechselwirkungen bezogenen Parameter reichten aus, um ein verlässliches Modell für das untersuchte System zu erzielen. rnDas umfassende Sampling des Phasenraumes der Systeme stellt aufgrund der zahlreichen Freiheitsgrade und der starken Interaktionen zwischen Calciumionen und Glutamat in Lösung eine besondere Herausforderung dar. Daher wurde die Methode der Biasing Potential Replica Exchange Molekular-Dynamik Simulationen im Hinblick auf das Sampling von Oligoglutamaten justiert und es erfolgte die Simulation von Peptiden verschiedener Kettenlängen in Anwesenheit von Calciumionen. Mit Hilfe der Sketch-Map Analyse konnten im Rahmen der Simulationen zahlreiche stabile Ionen-Peptid-Komplexe identifiziert werden, welche die Formation von Prä-Nukleations-Strukturen beeinflussen könnten. Abhängig von der Kettenlänge des Peptids weisen diese Komplexe charakteristische Abstände zwischen den Calciumionen auf. Diese ähneln einigen Abständen zwischen den Calciumionen in jenen Phasen von Calcium-Oxalat Kristallen, die in Anwesenheit von Oligoglutamaten gewachsen sind. Die Analogie der Abstände zwischen Calciumionen in gelösten Ionen-Peptid-Komplexen und in Calcium-Oxalat Kristallen könnte auf die Bedeutung von Ionen-Peptid-Komplexen im Prozess der Nukleation und des Wachstums von Biomineralen hindeuten und stellt einen möglichen Erklärungsansatz für die Fähigkeit von Oligoglutamaten zur Beeinflussung der Phase des sich formierenden Kristalls dar, die experimentell beobachtet wurde.

Antarctic cloud spectral emission from ground-based measurements, a focus on far infrared signatures

The present work belongs to the PRANA project, the first extensive field campaign of observation of atmospheric emission spectra covering the Far InfraRed spectral region, for more than two years. The principal deployed instrument is REFIR-PAD, a Fourier transform spectrometer used by us to study Antarctic cloud properties. A dataset covering the whole 2013 has been analyzed and, firstly, a selection of good quality spectra is performed, using, as thresholds, radiance values in few chosen spectral regions. These spectra are described in a synthetic way averaging radiances in selected intervals, converting them into BTs and finally considering the differences between each pair of them. A supervised feature selection algorithm is implemented with the purpose to select the features really informative about the presence, the phase and the type of cloud. Hence, training and test sets are collected, by means of Lidar quick-looks. The supervised classification step of the overall monthly datasets is performed using a SVM. On the base of this classification and with the help of Lidar observations, 29 non-precipitating ice cloud case studies are selected. A single spectrum, or at most an average over two or three spectra, is processed by means of the retrieval algorithm RT-RET, exploiting some main IR window channels, in order to extract cloud properties. Retrieved effective radii and optical depths are analyzed, to compare them with literature studies and to evaluate possible seasonal trends. Finally, retrieval output atmospheric profiles are used as inputs for simulations, assuming two different crystal habits, with the aim to examine our ability to reproduce radiances in the FIR. Substantial mis-estimations are found for FIR micro-windows: a high variability is observed in the spectral pattern of simulation deviations from measured spectra and an effort to link these deviations to cloud parameters has been performed.

Tradurre per le imprese. Analisi e traduzione in inglese della Nota integrativa al Bilancio consolidato 2013 di MNLG S.r.l.-Holding Sorma Group

The aim of this dissertation is to provide a translation in English of the Notes on the Consolidated Financial Statements of MNLG S.r.l., holding company of the Italian Sorma Group. This translation work is one example of the technical material produced in accordance with the project called Language Toolkit, set up by the Chamber of Commerce of Forlì-Cesena, to support the internationalization of the companies established in the territory. This initiative has represented a unique opportunity for me to put into practice the knowledge and abilities learnt in the translation field during these years at university. It also allowed me to give a concrete purpose to my dissertation, that is to provide a technical document translated into a foreign language. By making its Consolidated Financial Statement readily available in English, the company MNLG S.r.l. can in fact increase the number of possible investors and guarantee a more transparent financial informative to its shareholders. This translation work is divided into six chapters: the first one describes the project, its main objectives and the ways in which it was developed. The second chapter deals with the notions of Consolidated Financial Statements and presents the accounting documents of which the Financial Statements are made up as well as the norms according to which they are prepared. The third chapter, instead, focuses on the translation procedure applied and especially on the documentation process, analysing the differences between the International Accounting Standards and the accounting standards used in Italy. The fourth chapter provides a description of the translation resources built for the translation of this specific document. The fifth chapter includes the English version of the Notes on the Consolidated Financial Statements and, to conclude, the sixth chapter analyses the difficulties encountered in translating and the strategies adopted to overcome them.

Das deutsche Kriegsgefangenenwesen 1939 - 1945

Zusammenfassung: Die vorliegende Untersuchung zum deutschen Kriegsgefangenenwesen (KGW) im Zweiten Weltkrieg schließt eine wichtige Lücke innerhalb der geschichtswissenschaftlichen Forschungen zum Themenkreis der Kriegsgefangenschaft in deutschem Gewahrsam. Bisherige Studien (bis einschließlich 1997) behandeln vor allem sozial- und kulturgeschichtliche Aspekte der Kriegsgefangenen (Kgf.), der Lagergesellschaft und dem Alltag von Soldaten in Kriegsgefangenschaft. Der Verfasser indes legt mit seiner Magisterarbeit erstmals eine Organisations- und Strukturgeschichte des deutschen Kriegsgefangenenwesens von 1939 bis 1945 vor, welche fundamentale Grundlagen der deutschen militärischen Lagerorganisation und Verwaltung dokumentiert. So wird die Entwicklung von den Vorkriegsplanungen bis zum Kriegsende anhand der zentralen Dienststellen herausgearbeitet und im Kontext des Genfer Kriegsgefangenenabkommens von 1929 und völkerrechtlicher Implikationen gewichtet. Hiermit untrennbar verbundene Einflußnahmen nichtmilitärischer Stellen in die Entscheidungsgewalt der Streitkräfte im Heimatkriegsgebiet und in den Wehrmachtbefehlshaberbereichen werden nicht zuletzt auch anhand mehrerer Organigramme veranschaulicht. Zudem dokumentiert und analysiert die Untersuchung die im Kriegsverlauf stetig verschärften Maßnahmen zur Fluchtprävention und der konzertierten Fahndung nach geflohenen Kriegsgefangenen: Die Machterosion des Oberkommandos der Wehrmacht (OKW) zugunsten des Reichsführers-SS, des Reichssicherheitshauptamts und nicht zuletzt der Parteikanzlei der NSDAP wird so augenfällig. Trotz eminenter Schriftgutverluste kann der Verfasser vor allem anhand einer nahezu vollständig erhaltenen Schlüsselquelle die Stellenbesetzung und Organisationsstruktur der mit Kriegsgefangenenfragen befassten Stellen im OKW rekonstruieren. Die Auswertung dieser Sammelmitteilungen / Befehlssammlung für das Kriegsgefangenenwesen sowie an anderer Stelle überlieferter Organisationsbefehle ermöglicht wichtige Änderungen am derzeitigen Forschungsstand. Darüber hinaus beschäftigt sich die vorliegende Untersuchung mit dem Arbeitseinsatz Kriegsgefangener in der deutschen Wirtschaft als in der zweiten Kriegshälfte zentralem Element der Kriegsgefangenschaft. Außerdem wird beleuchtet, welche politischen, (rassen)ideologischen oder reziprok konnotierten Faktoren den Stellenwert gefangener Soldaten unterschiedlicher Nationalität innerhalb der Gefangenenhierarchie im deutschen Kriegsgefangenenwesen bestimmten. Inhalt: 1. Einführung; 2. Die Entwicklung des Kriegsvölkerrechts und das Genfer Kriegsgefangenenabkommen von 1929; 3. Einleitende Bemerkungen zum deutschen Kriegsgefangenenwesen: Quellenlage, Grundlagen; 4. Organisationsstruktur und Aufgaben des KGW: Zuständigkeiten für Kgf. in OKW und OKH, Abt. Wehrmachtverluste und Kriegsgefangene, der General z.b.V. für das KGW 1939 bis Ende 1941, Allgemeine und Organisationsabteilung seit Januar 1942, Generalinspekteur und Inspekteur des KGW von Juli 1943 bis Oktober 1944, das Kriegsgefangenenwesen unter Himmler seit Oktober 1944; 5. Die Kriegsgefangenenlager: Lagertypen, Anzahl und Verwendung, die Gesamtzahl Kgf. und Belegstärken ausgewählter Lager; 6. Richtlinien für KGL: Die Sammelmitteilungen / Befehlssammlung für das KGW, Lagerorganisation und Behandlung Kriegsgefangener; 7. Die Post der Kriegsgefangenen: Tätigkeit von Auslandsbriefprüfstelle, Abwehr III Referat Kgf. und Abwehrstellen der Wehrkreise, Vorgaben für Postüberwachung und Stimmungsberichte der Asten, Befehle zur Kgf-Post und Kooperation mit Hilfsorganisationen und Schutzmächten; 8. Fluchtprävention: Bestimmungen und Maßnahmen zur Fluchtvereitelung, der Fluchterlass vom 22.09.1942, der Sonderfahndungsplan der Sicherheitspolizei und des SD vom 28.09.1942, Erlass zur Kriegsfahndung vom 5.12.1942, der Fluchterlaß vom 02.07.1943, der Erlaß zur Mitarbeit NSDAP bei Groß- und Kriegsfahndungen vom 10.07.1943, Schulung zur Fluchtprävention auf Wehrkreisebene 1944, Preisausschreiben "Wie verhindere ich Fluchten?" vom 09.04.1945, Anwerbung von V-Leuten durch die Abwehr; 9. Arbeitseinsatz Kriegsgefangener in der deutschen Wirtschaft und beteiligte Stellen; 10. Der Status Kriegsgefangener unterschiedlicher Nationalitäten im Vergleich; 11. Schluss

La traduzione saggistica: tradurre il saggio Light Years Ahead

The aim of this dissertation is to demonstrate how theory and practice are linked in translation. The translation of the essay Light Years Ahead helped me to understand this connection and to develop the two main thesis included in this work, that is the possibility the translator has to choose among all the different theories, without giving one or another the absolute supremacy, and the diversity of the non-fiction genre. Therefore, the first chapter focuses on the different theories of translation, presented in a way which suggests that one might be the completion and the development of another. The second chapter deals with the peculiar issues of non-fiction translation, with particular attention to the way in which this genre gathers different elements of other text types. Despite this variety, it is also claimed that the function at the higher level of an essay is always the informative one. This concept led me to simplify and make more intelligible the Italian version of the text I translated (Light Years Ahead). In the third chapter, this last point is discussed, as well as my considerations about the function, the dominant aspect and the cultural analysis of the text, with particular regard to how the quality of the English translation affected my choices. In the fourth chapter I included some examples of translation, which best demonstrate the distinctive variety of styles of non-fiction texts and the possibility for the translator to choose each time which theory suits them best. Finally, I also included three examples which represent a sort of defeat for me, that is to say three points where the ambiguity of the text obliged me to remove that information for the sake of the dominant informative function.

Dalla gestione cartacea dei testi a quella digitale: lo stato dell'arte e possibili miglioramenti.

Questa tesi tratta la gestione dei formati digitali dei testi, parziale argomento del progetto Biblio dell'università di Bologna. L'analisi proposta in questa tesi prevede la proposta di un'architettura che sfrutta in parte tecnologie già esistenti come linguaggi di markup, gestione di frammenti di testo con XPointer e epubcfi, tools per NLP, TEI, DocBook. Questa architettura ha il compito di modificare i formati digitali dei documenti in modo tale che la struttura sia indipendente dall'impaginazione. Ciò avviene attraverso l'introduzione delle unità informative, ossia nuovi elementi nella struttura del testo. Le unità informative sono di vari tipi, quelle più rilevanti ed innovative riguardano parti di testo e periodi; esse, infatti, permettono di identificare un preciso periodo dall'opera senza che esso dipenda dal tipo di impaginazione. Per ottenere questo risultato sono state sollevate tre problematiche principali: la gestione delle opere già esistenti, la gestione delle traduzioni, la gestione di opere inedite; esse vengono rispettivamente risolte nelle proposte dei postprocessor, del translationSystem e dell'authorSystem. Tutte e tre si basano sulla produzione di un'enumerazione delle unità informative, con una particolare attenzione per i periodi. Per riuscire a reperire i periodi si sfruttano le tecnologie di riconoscimento NLP. Il translationSystem e l'authorSystem presentano inoltre funzioni per la gestione della numerazione. Inoltre si prende in considerazione un repository e un sistema di autenticazione certificato per combattere furti d'identità, plagi e simili. Comprende accenni al recupero di unità informative sulla base di FRBR e una proposta per un sistema multiautore.

Embodied computation and life: building blocks for open-ended evolution

Il presente lavoro si propone di sviluppare una analogia formale tra sistemi dinamici e teoria della computazione in relazione all’emergenza di proprietà biologiche da tali sistemi. Il primo capitolo sarà dedicato all’estensione della teoria delle macchine di Turing ad un più ampio contesto di funzioni computabili e debolmente computabili. Mostreremo quindi come un sistema dinamico continuo possa essere elaborato da una macchina computante, e come proprietà informative quali l’universalità possano essere naturalmente estese alla fisica attraverso questo ponte formale. Nel secondo capitolo applicheremo i risultati teorici derivati nel primo allo sviluppo di un sistema chimico che mostri tali proprietà di universalità, ponendo particolare attenzione alla plausibilità fisica di tale sistema.

Worldwide Diaspora of Aethina tumida (Coleoptera: Nitidulidae), a Nest Parasite of Honey Bees

Native to sub-Saharan Africa, Aethina tumida Murray (Coleoptera: Nitidulidae) is now an invasive pest of honey bee, Apis mellifera L., colonies in Australia and North America. Knowledge about the introduction (s) of this beetle from Africa into and among the current ranges will elucidate pest populations and invasion pathways and contribute to knowledge of how a parasite expands in new populations. We examined genetic variation in adult beetle samples from the United States, Australia, Canada, and Africa by sequencing a 912-base pair region of the mitochondrial DNA cytochrome c oxidase subunit I gene and screening 10 informative microsatellite loci. One Canadian introduction of small hive beetles can be traced to Australia, whereas the second introduction seems to have come from the United States. Beetles now resident in Australia were of a different African origin than were beetles in North America. North American beetles did not show covariance between two mitochondrial haplotypes and their microsatellite frequencies, suggesting that these beetles have a shared source despite having initial genetic structure within their introduced range. Excellent dispersal of beetles, aided in some cases by migratory beekeeping and the bee trade, seems to lead to panmixis in the introduced populations as well as in Africa.

Time-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation

Current methods to characterize mesenchymal stem cells (MSCs) are limited to CD marker expression, plastic adherence and their ability to differentiate into adipogenic, osteogenic and chondrogenic precursors. It seems evident that stem cells undergoing differentiation should differ in many aspects, such as morphology and possibly also behaviour; however, such a correlation has not yet been exploited for fate prediction of MSCs. Primary human MSCs from bone marrow were expanded and pelleted to form high-density cultures and were then randomly divided into four groups to differentiate into adipogenic, osteogenic chondrogenic and myogenic progenitor cells. The cells were expanded as heterogeneous and tracked with time-lapse microscopy to record cell shape, using phase-contrast microscopy. The cells were segmented using a custom-made image-processing pipeline. Seven morphological features were extracted for each of the segmented cells. Statistical analysis was performed on the seven-dimensional feature vectors, using a tree-like classification method. Differentiation of cells was monitored with key marker genes and histology. Cells in differentiation media were expressing the key genes for each of the three pathways after 21 days, i.e. adipogenic, osteogenic and chondrogenic, which was also confirmed by histological staining. Time-lapse microscopy data were obtained and contained new evidence that two cell shape features, eccentricity and filopodia (= 'fingers') are highly informative to classify myogenic differentiation from all others. However, no robust classifiers could be identified for the other cell differentiation paths. The results suggest that non-invasive automated time-lapse microscopy could potentially be used to predict the stem cell fate of hMSCs for clinical application, based on morphology for earlier time-points. The classification is challenged by cell density, proliferation and possible unknown donor-specific factors, which affect the performance of morphology-based approaches. Copyright © 2012 John Wiley & Sons, Ltd.

Dual origins of dairy cattle farming - evidence from a comprehensive survey of European Y-chromosomal variation

BACKGROUND: Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS: Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS: We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.

Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the "Beijing" sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.

CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE

Background Most adults infected with HIV achieve viral suppression within a year of starting combination antiretroviral therapy (cART). It is important to understand the risk of AIDS events or death for patients with a suppressed viral load. Methods and Findings Using data from the Collaboration of Observational HIV Epidemiological Research Europe (2010 merger), we assessed the risk of a new AIDS-defining event or death in successfully treated patients. We accumulated episodes of viral suppression for each patient while on cART, each episode beginning with the second of two consecutive plasma viral load measurements <50 copies/µl and ending with either a measurement >500 copies/µl, the first of two consecutive measurements between 50–500 copies/µl, cART interruption or administrative censoring. We used stratified multivariate Cox models to estimate the association between time updated CD4 cell count and a new AIDS event or death or death alone. 75,336 patients contributed 104,265 suppression episodes and were suppressed while on cART for a median 2.7 years. The mortality rate was 4.8 per 1,000 years of viral suppression. A higher CD4 cell count was always associated with a reduced risk of a new AIDS event or death; with a hazard ratio per 100 cells/µl (95% CI) of: 0.35 (0.30–0.40) for counts <200 cells/µl, 0.81 (0.71–0.92) for counts 200 to <350 cells/µl, 0.74 (0.66–0.83) for counts 350 to <500 cells/µl, and 0.96 (0.92–0.99) for counts ≥500 cells/µl. A higher CD4 cell count became even more beneficial over time for patients with CD4 cell counts <200 cells/µl. Conclusions Despite the low mortality rate, the risk of a new AIDS event or death follows a CD4 cell count gradient in patients with viral suppression. A higher CD4 cell count was associated with the greatest benefit for patients with a CD4 cell count <200 cells/µl but still some slight benefit for those with a CD4 cell count ≥500 cells/µl.

Mapping genetic variants associated with beta-adrenergic responses in inbred mice

β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS) addressing the values and susceptibility of cardiovascular-related traits to a selective β(1)-blocker, Atenolol (ate), and a β-agonist, Isoproterenol (iso). The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA), a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG) values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP) to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10(-8)). An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10(-6)). Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD). Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied.