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Whole genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ~80 million years ago (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one third reflect non-neutral tissue expression evolution, with strong purifying selection, maintained over ~50 million years. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates has evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points towards underlying differences in adaptive pressures on expression regulation in the non-anadromous grayling versus the anadromous Atlantic salmon.Our findings enhance our understanding of the role of WGD in genome evolution and highlights cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.

Copyright © 2017 The Authors, some rights reserved. Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations. Of special interest are genes and functional groups known to affect body patterning, beak morphology, and the immune system, which are important features of diversification and fitness. We show that a combination of mosaic parental inheritance and novel divergence within the hybrid lineage has facilitated the origin and maintenance of an avian hybrid species.

Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no., This work was supported by the Research Council of Norway (under grant agreements 221580, 218241, and 231217/F20), by the Norwegian Cancer Society (under grant agreements 71220’PR-2006-0433 and 3485238-2013), and by the South-Eastern Norway Regional Health Authority (under grant agreement 2014041).

Poster presented at the Biology Of Genomes meeting 2017

Definitions and experiment details. Formal definitions of terms used in the article and details on the section Genes on GRCh38 (pdf). (PDF 181 kb)

Figure S1. Reference fragments placement order depending on query fragment orientations during detection of local differences. Figure S2. Circular genome alignment alternatives. Figure S3. Number of differences in each category obtained by NucDiff with the default parameter settings for all assemblers. Figure S4. Comparison of multiple assemblies against one reference using NucDiff. Figure S5. Examples of detection of long deletions located in all assemblies at the same place in the reference sequence. Table S1. Alignment fragmentation cases caused by simple differences. Table S2. Genome modifications implemented during the simulation process. Table S3. List of E. coli genomes used in the Comparison of genomes from different strains of the same species section. Table S4. Parameter values used for each parameter settings. Table S5. Correspondence between the QUAST difference types and the simulated difference types. Table S6. Correspondence between the QUAST, dnadiff and NucDiff difference types and the expected difference types. (PDF 989 kb)

Genomic mosaicism and novel divergence have facilitated the creation and maintenance of a hybrid species, the Italian sparrow., Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations. Of special interest are genes and functional groups known to affect body patterning, beak morphology, and the immune system, which are important features of diversification and fitness. We show that a combination of mosaic parental inheritance and novel divergence within the hybrid lineage has facilitated the origin and maintenance of an avian hybrid species.

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Background: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

We present a set of computing tools and techniques that every researcher can and should adopt. These recommendations synthesize inspiration from our own work, from the experiences of the thousands of people who have taken part in Software Carpentry and Data Carpentry workshops over the past six years, and from a variety of other guides. Unlike some other guides, our recommendations are aimed specifically at people who are new to research computing., Comment: 19 pages, 1 figure

Background It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. Results We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. Conclusion More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .

Supplementary figures and tables. (PDF 647 kb)

The chloroplasts of heterokont algae such as diatoms are the result of a secondary endosymbiosis event, in which a red alga was engulfed by a non-photosynthetic eukaryote. The diatom chloroplast genomes sequenced to date show a high degree of similarity, but some examples of gene replacement or introduction of genes through horizontal gene transfer are known. The evolutionary origin of the gene transfers is unclear. We have sequenced and characterised the complete chloroplast genome and a putatively chloroplast-associated plasmid of the pennate diatom Seminavis robusta. The chloroplast genome contains two introns, a feature that has not previously been found in diatoms. The group II intron of atpB appears to be recently transferred from a Volvox-like green alga. The S. robusta chloroplast genome (150,905 bp) is the largest diatom chloroplast genome characterised to date, mainly due to the presence of four large gene-poor regions. Open reading frames (ORFs) encoded by the gene-poor regions show similarity to putative proteins encoded by the chloroplast genomes of different heterokonts, as well as the plasmids pCf1 and pCf2 found in the diatom Cylindrotheca fusiformis. A tyrosine recombinase and a serine recombinase are encoded by the S. robusta chloroplast genome, indicating a possible mechanism for the introduction of novel genes. A plasmid with similarity to pCf2 was also identified. Phylogenetic analyses of three ORFs identified on pCf2 suggest that two of them are part of an operon-like gene cluster conserved in bacteria. Several genetic elements have moved through horizontal gene transfer between the chloroplast genomes of different heterokonts. Two recombinases are likely to promote such gene insertion events, and the plasmid identified may act as vectors in this process. The copy number of the plasmid was similar to that of the plastid genome indicating a plastid localization.

Somatic cell count (SCC) is a diagnostic test of milk for mastitis in cows. Its specificity and sensitivity are less than 1.0, making test results uncertain. I discuss epistemological problems of the test such as underdetermination, undercalibration and underdiscrimination, in the solution of which biomedical and economic factors may play a role. Diagnostics of the SCC should be considered as an epistemological network, functioning in a network in which farmers, veterinarians, epidemiologists and milk industry shift their position following biomedical, technological and economic changes, which is described as an actor-network to understand how human and non-human agents in mastitis may be associated.

Background Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration. Results We here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff. Conclusions We have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on https://github.com/uio-cels/NucDiff under the MPL license.

Bacillus cereusstrains B06.009 and AH725 were isolated from human cerebrospinal fluid and eye infection, respectively. Here we present their annotated draft genome sequences, which are highly similar to environmentalB. cereusreference strains ATCC 10987 and ATCC 14579, underlining the opportunistic nature ofB. cereusinfections.

Genome-wide, cell-type-specific profiles are being systematically generated for numerous genomic and epigenomic features. There is, however, no universally applicable analytical methodology for such data. We present GSuite HyperBrowser, the first comprehensive solution for integrative analysis of dataset collections across the genome and epigenome. The GSuite HyperBrowser is an open-source system for streamlined acquisition and customizable statistical analysis of large collections of genome-wide datasets. The system is based on new computational and statistical methodologies that permit comparative and confirmatory analyses across multiple disparate data sources. Expert guidance and reproducibility are facilitated via a Galaxy-based web-interface. The software is available athttps://hyperbrowser.uio.no/gsuite

The paleoceanographic history of the Pacific Ocean during the mid-Cretaceous is poorly constrained due to the loss of much of the contemporaneous Pacific seafloor to subduction and difficulties in recovering chert-rich sediments by ocean drilling. Pelagic sediments that were originally deposited in the Pacific Ocean but that have been subsequently accreted during subduction potentially provide an alternative paleoceanographic archive. This study presents micropaleontological and carbon-isotope data from the Calera Limestone, part of the classic Franciscan Complex exposed in Permanente Quarry, central California, USA. In the three stratigraphic sections studied, pelagic limestones with low organic-carbon contents are the dominant lithology. However, two stratigraphic intervals are recognized that contain organic carbon, and these date to the early Aptian and late Albian-early Cenomanian. These time intervals correspond to two mid-Cretaceous oceanic anoxic events (OAEs): early Aptian OAE1a (equivalent to the "Selli level") and late Albian OAE1d (equivalent to the "Breistroffer event"). It is well established that both of these events were associated with significant carbon-isotope excursions, which are also shown to exist in the Calera Limestone. The record of OAE1a from the Calera Limestone complements ocean drilling records by providing further evidence for variability in the sedimentary and stratigraphic record of this event. The carbon-isotope data from the late Albian-early Cenomanian provide the first detailed chemobiostratigraphic record of this period for the Pacific Ocean, confirming that environmental change occurred at this time in the Pacific, possibly related to OAE1d. © 2008 Geological Society of America.

The Early Cretaceous Epoch, about 145-100 million years ago, is generally thought of as a greenhouse period, with high atmospheric CO 2 concentrations and high global mean temperatures. But evidence for episodes of cooler conditions, and even transient glaciations, has been proposed. Here we present sea-surface temperature records spanning the period from 142 to 128 million years ago (Berriasian-Barremian ages) from low and mid latitudes, reconstructed using the TEX 86 palaeotemperature proxy. During this period, we find sea-surface temperatures exceeding 32 °C at 15°-20° N and averaging 26 °C at ∼53° S. These temperatures substantially exceed modern temperatures at equivalent latitudes, and are incompatible with the notion of consistently cooler conditions in the earliest Cretaceous. Moreover, we find little variability in the sea-surface temperature records, even during the Valanginian carbon-isotope excursion ∼138-135 million years ago, which was thought to be associated with marked temperature fluctuations. We conclude that the earliest Cretaceous was characterized by a warm, stable climate, with a lower meridional temperature gradient than today. © 2011 Macmillan Publishers Limited. All rights reserved.

DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.

Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification. nivå2

Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users., The genome sequence is presented for the Atlantic salmon (Salmo salar), providing information about a rediploidization following a salmonid-specific whole-genome duplication event that resulted in an autotetraploidization. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users., A window on salmonid genome evolution William Davidson and colleagues report sequencing and assembly of the Atlantic salmon genome, which they demonstrate as a useful reference to also improve the genome assembly of other salmanoids. Their analyses provide insights into duplicate retention patterns across two rounds of whole-genome duplication that have occurred in this lineage. Supplementary information The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users.

The genome of Atlantic cod (Gadus morhua L.) published in 2011 was the first example of a teleost genome obtained using a pure high-throughput sequencing (HTS) technology strategy, and the first large vertebrate genome generated by exclusively using Roche/454 sequencing technology. At the start of the sequencing project in 2009, two HTS technologies were available, the Roche/454 and Illumina technologies. Because of the longer read length of the Roche/454 technology and a wider range of suitable software utilizing those data at the time, we chose to use this technology for the first version of the Atlantic cod genome. In this chapter, we describe the process leading to the assembly and annotation of the first Atlantic cod genome. Since the release in 2011, spectacular developments in sequencing technologies and assembly software have allowed for a second, improved version of the Atlantic cod genome—which will be further described in the Atlantic cod genome chapter ( Chapter 3 ). Although rather fragmented according to current standards, our first genome assembly has proven to be an important resource for the community—as illustrated by its extensive use in a wide range of studies and it catalyzing new projects and research funding.

My Sept. 28, 2016 "Balti and Bioinformatics" talk. Video recording: https://www.youtube.com/watch?v=J_ZY9_OyRhE (second talk)See also http://lab.loman.net/balti/2016/07/09/balti-and-bioinformatics-28th-september-2016/

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Slides of the presentation I gave at the SMRT Scientific Symposium, Leiden, The Netherlands on June 6, 2016

Recent advancements within state-of-the-art genomic tools and the generation of the first version of the Atlantic cod genome (Star et al., 2011) have proven to be valuable resources, improving our understanding of this species’ biology. In this chapter we describe some aspects and implications of using these resources to identify genes and molecular pathways involved in Atlantic cod growth and development, as well as responses to nutritional changes, pathogens and other immune stimuli, and environmental stressors (e.g., temperature, stress, or pollutants). Additionally, we highlight the immunological puzzle of the Atlantic cod that lacks components of the adaptive immune system previously thought to be an essential feature of all jawed vertebrates. Furthermore, we present a new and substantially improved version of the Atlantic cod genome by combining recent developments within bioinformatics tools and the inclusion of data from both short as well as long read sequencing technologies. The new version of the Atlantic cod genome will be of high impact; facilitating applied functional genomics research to improve our understanding of gene function and variants affecting important phenotypic traits such as growth, sexual maturation, and disease resistance. Moreover, large-scale resequencing efforts of selected specimens would further aid in deducing genomic effects of natural selection, identifying specific changes involved in local adaptation in the wild as well as in artificial selection related to breeding programs. This will allow for a systems biology approach where effects of a large number of gene variants (and regulatory pathways) can be causally related to phenotypic variation, for example, knowledge that will be crucial in selecting family material for the emerging cod aquaculture.

A variety of sex determination mechanisms can be observed in evolutionary divergent teleosts. Sex determination is genetic in Atlantic cod (Gadus morhua), however the genomic location or size of its sex-locus is unknown. Here, we characterize the sex-locus of Atlantic cod using whole genome sequence (WGS) data of 227 wild-caught specimens. Analyzing more than 55 million polymorphic loci, we identify 166 loci that are associated with sex. These loci are located in six distinct regions on five different linkage groups (LG) in the genome. The largest of these regions, an approximately 55 Kb region on LG11, contains the majority of genotypes that segregate closely according to a XX-XY system. Genotypes in this region can be used genetically determine sex, whereas those in the other regions are inconsistently sex-linked. The identified region on LG11 and its surrounding genes have no clear sequence homology with genes or regulatory elements associated with sex-determination or differentiation in other species. The functionality of this sex-locus therefore remains unknown. The WGS strategy used here proved adequate for detecting the small regions associated with sex in this species. Our results highlight the evolutionary flexibility in genomic architecture underlying teleost sex-determination and allow practical applications to genetically sex Atlantic cod.

8 pages, 1 table, The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field. © 2012 Elsevier B.V., The Department of Biology, University of Oslo, MLSUIO (Molecular Life Science) and ForBio (Norwegian–Swedish Research School in Biosystematics) are acknowledged for financial support, enabling the preparation of this work. R.L. has been financed by a Marie Curie Intra-European Fellowship grant PIEF-GA-2009-235365. T.H.A.H. has been supported with a VISTA/Statoil grant project number 6503

This study develops a method for calculating the precision with which a cutting tool can be set along the axis of rotation of a B-axis rotary table on a lathe. The uncertainty with which the tool can be set on the rotary table is calculated from knowledge of the machine tool, the probing system, and the effects of the environment. Three common tool-setting techniques are analyzed as examples. The techniques analyzed are a touch probe tool set station, a technique that machines grooves in the face of a workpiece and then measures the relative depths of the grooves, and an optical tool set station that uses a video camera looking down onto the rake face of the cutting tool. Experiments using these three example techniques reveal the precision with which a tool can be set. For each technique, the predicted tool setting uncertainties agree with the experimentally determined values. Therefore, this method can estimate how well a tool can be set along the axis of rotation of a B-axis rotary table for a particular application, without the need for extensive tool setting experiments.

The contribution of wound contraction to wound closure determines the speed of second intention wound healing and it has been shown that significant differences exist with regard to both contraction and inflammatory response between horses and ponies and between various areas of the body. In this study, the contraction capacity of fibroblasts from limbs and buttocks of 4 Dutch Warmblood horses and 4 Shetland ponies was studied in vitro, in order to determine whether differences in wound contraction are due to differences in the inherent contraction capacity of the fibroblasts or to differences in tissue environmental factors, such as the inflammatory response. Fibroblasts were harvested from subcutaneous tissue, cultured and then suspended in both floating and anchored collagen gels. Contraction capacity was assessed by measuring the decrease in area of the floating gels and by measuring the microforces generated in the anchored gels using a custom-built measuring device. In the floating gels, no difference existed in the contraction capacity of fibroblasts from horses and ponies, or from limbs and buttocks. In the anchored gels, no differences existed between horse and pony fibroblasts, but the fibroblasts from the limbs started to contract significantly sooner and produced significantly higher forces than those from the buttocks. It is concluded that the in vivo differences in wound contraction between horses and ponies and between different sites of the body are not caused by differences in the inherent contraction capacity of fibroblasts. The in vitro differences between fibroblasts from limbs and buttocks are thought to be due to the lower proliferation rate and the longer culture time of the fibroblasts originating from the limbs, because mature fibroblasts can develop higher contraction forces than immature fibroblasts. This means that tissue environmental factors, such as cytokine profiles during the inflammatory response, determine the extent of contraction during wound healing. Further research should be directed towards the role of the inflammatory response in wound healing.