Design of a Hand Held Minimally Invasive Lung Tumour Localization Device

Lung cancer is the leading type of cancer that causes death. If diagnosed, the treatment of choice is surgical resection of the tumour. Traditionally, a surgeon feels for the presence of a tumour in open thoracic surgery. However, a minimally invasive approach is desired. A major problem presented by the minimally invasive approach is the localization of the tumour. This project describes the design, analysis, and experimental validation of a novel minimally invasive instrument for lung tumour localization. The instrument end effector is a two degree of freedom lung tissue palpator. It allows for optimal tissue palpation to increase useful sensor feedback by ensuring sensor contact, and prevents tissue damage by uniformly distributing pressure on the tissue with an upper bound force. Finite element analysis was used extensively to guide the design process. The mechanism is actuated using high strength tungsten cables attached to controlled motors. Heat treatment experiments were undertaken with stainless steel alloy 440C for use in the design, achieving a device factor of safety of 4. This factor of safety is based on a 20 N force on the end effector — the approximate weight of a human lung. The design was prototyped and validation experiments were carried out to assess its articulation and its load carrying capacity. Up to 10 N of force was applied to the prototype. Issues to resolve in the current design include cable extension effects and the existence of joint inflection. The end effector was also designed to allow the inclusion of ultrasound, tactile, and kinaesthetic sensors. It is hypothesized that a plurality of sensors will increase the likelihood of positive tumour localization. These sensors, combined with the presented mechanical design, form the basis for research in robotics-assisted palpation. A proof of concept control system is presented for automated palpation

Developing novel bioinformatics tools and pipelines for working with reference genomes and large sets of resequenced genomes.

Both reference genomes assembled for individual species and large, publicly maintained sets of resequenced genomes are of immense value to researchers. The former represent important milestones for research involving the species of interest and serve as ostensibly static points of reference for other data, while the latter serve as catalogues of genetic variation, enabling researchers to place their own data in a wider context. However, maintaining sets of resequenced genomes and ensuring their integrity as they undergo updates to match any new releases of their reference genome poses certain computational challenges, as does manipulating and comparing those large sets of genomes in general. This work reports on the detection and correction of significant errors which were introduced into resequenced tomato data in the course of updating them to a new version. It also introduces Tersect, a low-level utility optimized for manipulating and comparing large sets of resequenced genomic data, as well as Tersect Browser, a Web application which uses the high performance of Tersect, coupled with a higher-level indexing and precomputation scheme to allow for interactive comparison of large sets of resequenced genomes, giving biologists a tool capable of generating visualisations of genetic distance and phylogenetic relationships based on whole-genome sequence data from hundreds of genomes in seconds rather than hours.PhD in Environment and Agrifoo

New Science Gateways for Advanced Computing Simulations and Visualization Using Vine Toolkit in PL-Grid

A Science Gateway is a connection between scientists and their computational tools in the form of web portal. It creates a space for communities, collaboration and data sharing and visualization in a comprehensive and efficient manner. The main purpose of such a solution is to allow users to access the computational resources, process and analyze their data and get the results in a uniform and user friendly way. In this paper we propose a complex solution based on the Rich Internet Application (RIA) approach consisting of a web portal powered by Vine Toolkit with Adobe Flex/BlazeDs technologies. There are two Science Gateways described in detail one for engineers to manage computationally intensive workflows used in advanced airplane construction simulations, and one for nanotechnology scientists to manage experiments in nano-science field calculated with Density Functional Theory (DFT). In both cases the results show how modern web solution can help scientists in their work. &nbsp

Tersect: a set theoretical utility for exploring sequence variant data

Comparing genomic features among a large panel of individuals across the same species is considered nowadays a core part of the bioinformatics analyses. This typically involves a series of complex theoretical expressions to compare, intersect, extract symmetric differences between individuals within a large set of genotypes. Several publically available tools are capable of performing such tasks; however, due to the sheer size of variants being queried, such tasks can be computationally expensive with a runtime ranging from few minutes up to several hours depending on the dataset size. This makes existing tools unsuitable for interactive data query or as part of genomic data visualization platforms such as genome browsers. Tersect is a lightweight, high-performance command-line utility which interprets and applies flexible set theoretical expressions to sets of sequence variant data. It can be used both for interactive data exploration and as part of a larger pipeline thanks to its highly optimized storage and indexing algorithms for variant data

Changes in soil microbial communities as a result of growing Brassicaceae crops

The study was conducted in 2006 - 2008 at the Production and Experimental Station of the University of Warmia and Mazury in Olsztyn, located in Bałcyny (NE Poland). The objective of this study was to determine the microbial quality of soil after Brassicaceae grown as forecrops for winter wheat. A field experiment was established on grey-brown podsolic soil, and it involved the following forecrops: winter rapeseed, spring rapeseed, white mustard, Chinese mustard, and winter wheat as control. Soil samples for microbiological analyses were collected in the spring, before the sowing of forecrops, and in the autumn, after the harvest of Brassicaceae and ploughing-in crop residues. Bacterial and fungal communities isolated from soil sown with Brassicaceae as forecrops were generally more abundant and diverse. These communities exerted an inhibitory effect on the growth of soil pathogens. Forecrops with the greatest microbiological potential were white mustard and winter rapeseed

De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

Motivation: Solanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Results: A high-quality de novo genome and transcriptome assembly for S. sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (~159X coverage) and PacBio long reads (~44X coverage), generating a total of ~262 Gbp of DNA sequence. A reference genome of 1,245 Mbp, arranged in 1,483 scaffolds with a N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, ~63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7. Availability: S. sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI’s Sequence Read Archive, under the BioProject number “PRJNA633104”

BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene

A mutant line, bifurcate flower truss (bif), was recovered from a tomato breeding program. Plants from the control line LAM183 produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The LAM183 and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a MAP kinase, contained a leucine-to-stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato

Missense mutation of a class B heat shock factor is responsible for the tomato bushy root-2 phenotype

The bushy root-2 (brt-2) tomato mutant has twisting roots, and slower plant development. Here we used whole genome resequencing and genetic mapping to show that brt-2 is caused by a serine to cysteine (S75C) substitution in the DNA binding domain (DBD) of a heat shock factor class B (HsfB) encoded by SolycHsfB4a. This gene is orthologous to the Arabidopsis SCHIZORIZA gene, also known as AtHsfB4. The brt-2 phenotype is very similar to Arabidopsis lines in which the function of AtHsfB4 is altered: a proliferation of lateral root cap and root meristematic tissues, and a tendency for lateral root cap cells to easily separate. The brt-2 S75C mutation is unusual because all other reported amino acid substitutions in the highly conserved DBD of eukaryotic heat shock factors are dominant negative mutations, but brt-2 is recessive. We further show through reciprocal grafting that brt-2 exerts its effects predominantly through the root genotype even through BRT-2 is expressed at similar levels in both root and shoot meristems. Since AtHsfB4 is induced by root knot nematodes (RKN), and loss-of-function mutants of this gene are resistant to RKNs, BRT-2 could be a target gene for RKN resistance, an important trait in tomato rootstock breeding.Biotechnology and Biological Sciences Research Council (BBSRC): BB/L01954X/

Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant

The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.The research was supported by BBSRC—UKRI funding; the RootLINK (BB/L01954X/1) and AdRoot (BB/S007970/1) projects