Detection of dead standing Eucalyptus camaldulensis without tree delineation for managing biodiversity in native Australian forest

In Australia, many birds and arboreal animals use hollows for shelters, but studies predict shortage of hollows in near future. Aged dead trees are more likely to contain hollows and therefore automated detection of them plays a substantial role in preserving biodiversity and consequently maintaining a resilient ecosystem. For this purpose full-waveform LiDAR data were acquired from a native Eucalypt forest in Southern Australia. The structure of the forest significantly varies in terms of tree density, age and height. Additionally, Eucalyptus camaldulensis have multiple trunk splits making tree delineation very challenging. For that reason, this paper investigates automated detection of dead standing Eucalyptus camaldulensis without tree delineation. It also presents the new feature of the open source software DASOS, which extracts features for 3D object detection in voxelised FW LiDAR. A random forest classifier, a weighted-distance KNN algorithm and a seed growth algorithm are used to create a 2D probabilistic field and to then predict potential positions of dead trees. It is shown that tree health assessment is possible without tree delineation but since it is a new research directions there are many improvements to be made

Identification of genes coding for B cell antigens of Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC) by using phage display

<p>Abstract</p> <p>Background</p> <p>Contagious bovine pleuropneumonia (CBPP) is a mycoplasmal disease caused by <it>Mycoplasma mycoides </it>subsp. <it>mycoides </it>SC (<it>Mmm</it>SC). Since the disease is a serious problem that can affect cattle production in parts of Africa, there is a need for an effective and economical vaccine. Identifying which of the causative agent's proteins trigger potentially protective immune responses is an important step towards developing a subunit vaccine. Accordingly, the purpose of this study was to determine whether phage display combined with bioinformatics could be used to narrow the search for genes that code for potentially immunogenic proteins of <it>Mmm</it>SC. Since the production of IgG2 and IgA are associated with a Th₁cellular immune response which is implicated in protection against CBPP, antigens which elicit these immunoglobulin subclasses may be useful in developing a subunit vaccine.</p> <p>Results</p> <p>A filamentous phage library displaying a repertoire of peptides expressed by fragments of the genome of <it>MmmSC </it>was constructed. It was subjected to selection using antibodies from naturally- and experimentally-infected cattle. Mycoplasmal genes were identified by matching the nucleotide sequences of DNA from immunoselected phage particles with the mycoplasmal genome. This allowed a catalogue of genes coding for the proteins that elicited an immune response to be compiled. Using this method together with computer algorithms designed to score parameters that influence surface accessibility and hence potential antigenicity, five genes (<it>abc, gapN, glpO, lppB </it>and <it>ptsG</it>) were chosen to be expressed in <it>Escherichia coli</it>. After appropriate site-directed mutagenesis, polypeptides representing portions of each of these proteins were tested for immunoreactivity. Of these five, polypeptides representing expression products of <it>abc </it>and <it>lppB </it>were recognised on immunoblots by sera obtained from cattle during a natural outbreak of the disease.</p> <p>Conclusion</p> <p>Since phage display physically couples phenotype with genotype, it was used to compile a list of sequences that code for <it>Mmm</it>SC proteins bearing epitopes which were recognised by antibodies in the serum of infected animals. Together with the appropriate bioinformatic analyses, this approach provided several potentially useful vaccine or diagnostic leads. The phage display step empirically identified sequences by their interaction with antibodies which accordingly reduced the number of ORFs that had to be expressed for testing. This is a particular advantage when working with <it>Mmm</it>SC since the mycoplasmal codon for tryptophan needs to be mutated to prevent it from being translated as a stop in <it>E. coli</it>.</p

Alignment of hyperspectral imagery and full-waveform LIDAR data for visualisation and classification purposes

The overarching aim of this paper is to enhance the visualisations and classifications of airborne remote sensing data for remote forest surveys. A new open source tool is presented for aligning hyperspectral and full-waveform LiDAR data. The tool produces coloured polygon representations of the scanned areas and aligned metrics from both datasets. Using data provided by NERC ARSF, tree coverage maps are generated and projected into the polygons. The 3D polygon meshes show well-separated structures and are suitable for direct rendering with commodity 3D-accelerated hardware allowing smooth visualisation. The intensity profile of each wave sample is accumulated into a 3D discrete density volume building a 3D representation of the scanned area. The 3D volume is then polygonised using the Marching Cubes algorithm. Further, three user-defined bands from the hyperspectral images are projected into the polygon mesh as RGB colours. Regarding the classifications of full-waveform LiDAR data, previous work used extraction of point clouds while this paper introduces a new approach of deriving information from the 3D volume representation and the hyperspectral data. We generate aligned metrics of multiple resolutions, including the standard deviation of the hyperspectral bands and width of the reflected waveform derived from the volume. Tree coverage maps are then generated using a Bayesian probabilistic model and due to the combination of the data, higher accuracy classification results are expected

Evaluation of Performance of Matured Hydraulic Grouts: Strength Development, Microstructural Characteristics and Durability Issues

The present paper evaluates the performance of matured hydraulic grouts, with respect to their composition and the induced microstructural characteristics. Four different grout compositions were examined; three grouts based on natural hydraulic lime (NHL5), plain and in combination with pozzolan, and a ternary white cement - pozzolan - hydrated lime mixture. Both grout-only specimens and composite injected material have been examined and injected grout - masonry material interaction issues are discussed

Short communication: Identification of variation in the ovine prolactin gene of Chios sheep with a cost-effective sequence-based typing assay

The present study identified single nucleotide polymorphisms (SNP) in the coding and untranslated regions of the ovine prolactin gene of Chios sheep. By developing a cost-effective direct sequence-based typing assay, around 600 bp of reliable sequencing data and clear identification of heterozygous positions was achieved. Five SNP were found, located in exons 2 (KC764410:g.567G>A, g.625C>T, g.683C>A) and 3 (KC764410:g.2015C>A, g.2101G>A), whereas the remaining exons were monomorphic. The identified SNP were synonymous, with the exception of the g.567G>A SNP, which results in an Arg to His amino acid change. As the sequencing cost of the sequence-based typing assay was 20 orders of magnitude lower compared with a standard Sanger method, the assay was also used as a genotyping tool. The identified polymorphism was genotyped for 247 ewes and was subsequently used in mixed model association analyses of milk yield, milk fat content, and litter size at birth. The association analysis revealed a significant dominance effect of 0.17 ± 0.07 of the g.2015C>A SNP on milk fat percentage, whereas a dominance effect of −21.33 ± 10.51 of the same SNP on total lactation milk yield was also estimated. The g.2015C>A SNP explained 2.47 and 3.68% of the total phenotypic variance of milk yield and milk fat percentage, respectively, whereas the corresponding values for the animal variance were 7.14 and 11.75%. A suggestive association of the nonsynonymous g.567G>A SNP with litter size at birth was also detected

Population genetics and demography of the endemic mouse species of Cyprus, Mus cypriacus

Mus cypriacus is one of three small palaeoendemic mammals that have survived the Mediterranean islands’ anthropization. This species, endemic to Cyprus, was described in 2006 and stands out as one of the last mammal species to have been discovered in Europe. Despite scarce data on its genetics, ecology, and life-history traits, Mus cypriacus is assessed as Least Concern LC in the IUCN Red List, partly due to its morphological similarity with the sympatric house mouse that prevented earlier identification. Our study uses mitochondrial and microsatellite markers to investigate this small rodent's population genetic structure and diversity. Our analysis did not identify any population genetic structure and suggested a high genetic diversity across Cyprus. When inferring habitat preference using sample locations, it appeared that M. cypriacus utilizes a diverse variety of habitats, covering more than 80% of the island. Although these results are encouraging for the conservation status of the species, they still need to be cautiously applied as potential threats may arise due to increasing habitat destruction and changes in land use. Consequently, our encouraging results should be applied judiciously. Additional ecological data are urgently needed to gain a more comprehensive understanding of this inconspicuous endemic species

Selection Signatures in Worldwide Sheep Populations

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments

Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep

Milk yield is the most important dairy sheep trait and constitutes the key genetic improvement goal via selective breeding. Mastitis is one of the most prevalent diseases, significantly impacting on animal welfare, milk yield and quality, while incurring substantial costs. Our objectives were to determine the feasibility of a concomitant genetic improvement programme for enhanced milk production and resistance to mastitis. Individual records for milk yield, and four mastitis-related traits (milk somatic cell count, California Mastitis Test score, total viable bacterial count in milk and clinical mastitis presence) were collected monthly throughout lactation for 609 ewes of the Chios breed. All ewes were genotyped with a mastitis specific custom-made 960 single nucleotide polymorphism (SNP) array. We performed targeted genomic association studies, (co)variance component estimation and pathway enrichment analysis, and characterised gene expression levels and the extent of allelic expression imbalance. Presence of heritable variation for milk yield was confirmed. There was no significant genetic correlation between milk yield and mastitis traits. Environmental factors appeared to favour both milk production and udder health. There were no overlapping of SNPs associated with mastitis resistance and milk yield in Chios sheep. Furthermore, four distinct Quantitative Trait Loci (QTLs) affecting milk yield were detected on chromosomes 2, 12, 16 and 19, in locations other than those previously identified to affect mastitis resistance. Five genes (DNAJA1, GHR, LYPLA1, NUP35 and OXCT1) located within the QTL regions were highly expressed in both the mammary gland and milk transcriptome, suggesting involvement in milk synthesis and production. Furthermore, the expression of two of these genes (NUP35 and OXCT1) was enriched in immune tissues implying a potentially pleiotropic effect or likely role in milk production during udder infection, which needs to be further elucidated in future studies. In conclusion, the absence of genetic antagonism between milk yield and mastitis resistance suggests that simultaneous genetic improvement of both traits be achievable

Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep

Stefan Hiendleder is a member of the International Sheep Genomics ConsortiumIn sheep, small ruminant lentiviruses cause an incurable, progressive, lymphoproliferative disease that affects millions of animals worldwide. Known as ovine progressive pneumonia virus (OPPV) in the U.S., and Visna/Maedi virus (VMV) elsewhere, these viruses reduce an animal’s health, productivity, and lifespan. Genetic variation in the ovine transmembrane protein 154 gene (TMEM154) has been previously associated with OPPV infection in U.S. sheep. Sheep with the ancestral TMEM154 haplotype encoding glutamate (E) at position 35, and either form of an N70I variant, were highly-susceptible compared to sheep homozygous for the K35 missense mutation. Our current overall aim was to characterize TMEM154 in sheep from around the world to develop an efficient genetic test for reduced susceptibility. The average frequency of TMEM154 E35 among 74 breeds was 0.51 and indicated that highly-susceptible alleles were present in most breeds around the world. Analysis of whole genome sequences from an international panel of 75 sheep revealed more than 1,300 previously unreported polymorphisms in a 62 kb region containing TMEM154 and confirmed that the most susceptible haplotypes were distributed worldwide. Novel missense mutations were discovered in the signal peptide (A13V) and the extracellular domains (E31Q, I74F, and I102T) of TMEM154. A matrix-assisted laser desorption/ionization–time-of flight mass spectrometry (MALDI-TOF MS) assay was developed to detect these and six previously reported missense and two deletion mutations in TMEM154. In blinded trials, the call rate for the eight most common coding polymorphisms was 99.4% for 499 sheep tested and 96.0% of the animals were assigned paired TMEM154 haplotypes (i.e., diplotypes). The widespread distribution of highly-susceptible TMEM154 alleles suggests that genetic testing and selection may improve the health and productivity of infected flocks.Michael P. Heaton, Theodore S. Kalbfleisch, Dustin T. Petrik, Barry Simpson, James W. Kijas, Michael L. Clawson, Carol G. Chitko-McKown, Gregory P. Harhay, Kreg A. Leymaster, the International Sheep Genomics Consortiu