Enhancing metabolite coverage in MALDI-MSI using laser post-ionisation (MALDI-2).

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) of metabolites can reveal how metabolism is altered throughout heterogeneous tissues. Here negative ion mode MALDI-MSI has been coupled with laser post-ionisation (MALDI-2) and applied to the MSI of low molecular weight (LMW) metabolites (

Trapping as an alternative method of eradicating classical swine fever in a wild boar population in Bulgaria.

Between August and November 2009, eight cases of classical swine fever (CSF) occurred in young wild boar in a 25-km2 oak forest3 km south of the river Danube in the north-eastern part of Bulgaria. The wild boar population within the affected area was estimated to be 156 animals, or approximately six boar per km2. To control and eradicate the disease, and in addition to vaccination and hunting, trapping was used to reduce the boar population to below two animals per km2. In total, 124 wild boar were removed from the infected area within three months. Of these, 119 were trapped. In this paper, the authors present trapping as a successful tool to eradicate CSF from an area where hunting and vaccination alone might not be sufficient. Up to seven wild boar could be trapped in a single trap. Furthermore, the spread of CSF virus to the local domestic pig population and to wild boar in neighbouring areas was prevented. By decreasing the wild boar population to fewer than two animals per km2, it was assumed that the virus would no longer circulate and the disease would fade out. In fact, no further CSF cases were diagnosed afterwards. Under Bulgarian and similar conditions, trapping seems to be a more reliable method than hunting for reducing a wild boar population within a short period of time. Furthermore, trapping may be used alone or in combination with hunting, depending on the situation.

Field observations and experiences gained from the implementation of control measures against lumpy skin disease in South-East Europe between 2015 and 2017.

The first epidemics of lumpy skin disease (LSD) reported in Europe in 2015 severely affected the cattle farming sector in several Balkan countries. After the first incursion into Greece in 2015, the disease quickly spread across the Balkan region with over 7000 outbreaks reported by the end of 2016. Thanks to a coordinated regional control and eradication policy, the spread of the disease was halted by the end of 2017. Regional large-scale vaccination campaign with effective homologous vaccines and high vaccination coverage revealed to be essential for the successful control the disease, supported by other measures such as early detection of outbreaks, total or partial stamping out and restrictions on cattle movements. The aim of this paper is to discuss the field observations, challenges and lessons learnt while dealing with the first LSD epidemics in Europe. The cross-border collaboration by the veterinary authorities of all affected countries, coordinated by the European Commission and the technical support provided by many other international organizations played a fundamental role in stopping the spread of a disease that otherwise could have expanded further to the European territory causing a large damage to the whole European cattle farming industry. The experience obtained during the control of LSD epidemics indicates that in the future LSD spread can be effectively halted, provided that appropriate surveillance plans and vigilance remains in place in the areas at risk of re-incursion, especially those bordering endemic countries.

Suitability of group-level oral fluid sampling in ruminant populations for lumpy skin disease virus detection.

The geographic expansion of Lumpy skin disease (LSD) from the near East into the European Union highlighted again the need for appropriate disease detection tools applicable to animal host populations where access to individual animals is difficult. This is of particular importance considering that the clinical manifestation of LSD is often mild making early disease detection challenging under the above-mentioned conditions. Building on positive experiences of group-level oral fluid sampling for pathogen detection as it is known to work for swine herds and wild boar, the concept was transferred to ruminants. Two groups of six cattle were infected experimentally with Lumpy skin disease virus (LSDV) under controlled conditions. Blood as well as oropharyngeal and nasal swab samples were collected at regular intervals. Group samples were obtained by placing cotton gauze around a salt lick block provided commonly as dietary supplement. Pieces of the gauze with visible signs of manipulation were tested in parallel to samples obtained from individual animals. Genome load analysis by qPCR technology revealed LSDV detection window starting from day 2 post infection until day 28 post infection, the end of the animal trial. At the individual level, detection periods varied between animals and type of sample and included intermitted detection. The accumulative character of the alternative sampling method makes it suitable to detect LSDV DNA at group-level even at times of the infection where a selective sampling of individuals from a group - as normally done in LSD surveillance - would have most likely failed in the detection.

Assessing the potential spread and maintenance of foot-and-mouth disease virus infection in wild ungulates: general principles and application to a specific scenario in Thrace.

Foot-and-mouth disease (FMD), due to infection with serotype O virus, occurred in wild boar and within eleven outbreaks in domestic livestock in the south-east of Bulgaria, Thrace region, in 2011. Hence, the issue of the potential for the spread and maintenance of FMD virus (FMDV) infection in a population of wild ungulates became important. This assessment focused on the spread and maintenance of FMDV infection within a hypothetical wild boar and deer population in an environment, which is characterized by a climate transitional between Mediterranean and continental and variable wildlife population densities. The assessment was based on three aspects: (i) a systematic review of the literature focusing on experimental infection studies to identify the parameters describing the duration of FMDV infection in deer and wild boar, as well as observational studies assessing the occurrence of FMDV infection in wild deer and wild boar populations, (ii) prevalence survey data of wild boar and deer in Bulgaria and Turkey and (iii) an epidemiological model, simulating the host-to-host spread of FMDV infections. It is concluded, based on all three aspects, that the wildlife population in Thrace, and so wildlife populations in similar ecological settings, are probably not able to maintain FMD in the long term in the absence of FMDV infection in the domestic host population. However, limited spread of FMDV infection in time and space in the wildlife populations can occur. If there is a continued cross-over of FMDV between domestic and wildlife populations or a higher population density, virus circulation may be prolonged.

Super-resolution segmentation of imaging mass spectrometry data: Solving the issue of low lateral resolution.

In the last decade, imaging mass spectrometry has seen incredible technological advances in its applications to biological samples. One computational method of data mining in this field is the spatial segmentation of a sample, which produces a segmentation map highlighting chemically similar regions. An important issue for any imaging mass spectrometry technology is its relatively low spatial or lateral resolution (i.e. a large size of pixel) as compared with microscopy. Thus, the spatial resolution of a segmentation map is also relatively low, that complicates its visual examination and interpretation when compared with microscopy data, as well as reduces the accuracy of any automated comparison. We address this issue by proposing an approach to improve the spatial resolution of a segmentation map. Given a segmentation map, our method magnifies it up to some factor, producing a super-resolution segmentation map. The super-resolution map can be overlaid and compared with a high-res microscopy image. The proposed method is based on recent advances in image processing and smoothes the "pixilated" region boundaries while preserving fine details. Moreover, it neither eliminates nor splits any region. We evaluated the proposed super-resolution segmentation approach on three MALDI-imaging datasets of human tissue sections and demonstrated the superiority of the super-segmentation maps over standard segmentation maps.

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns.

We present investigation of gene expression profiles by means of singular spectrum analysis (SSA). The biological problem under investigation is the decomposition of bicoid protein profiles of Drosophila melanogaster into the sum of a signal and noise, where the former consists of an exponential-in-distance pattern and is close to constant nonspecific component, or "background." The signal processing problems addressed are (i) trend extraction from a noisy signal, (ii) batch processing of similar data, and (iii) analytical approximation of the signal components by the sum of exponential and constant-like functions. The proposed methods are evaluated on the given 17 series.