Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven hemiascomycete yeast species. Three of these genomes are polyploid, and hence contain intra-genomic syntenic regions, the correct assembly of which is a particular success of YGOB. Designed to accurately assemble, display and score gene order relationships, YGOB is both an interactive tool for browsing genomic data, and a software engine now being used for evolutionary analyses on a whole-genome scale. Underlying the online interface is the YGOB database, which consists of homology assignments across the species, extensively curated based on sequence similarity and novelly, an appraisal of genomic context (synteny) in multiple genomes. Currently the YGOB database incorporates genome data from Saccharomyces cerevisiae, Candida glabrata, Saccharomyces castellii, Ashbya gossypii, Kluyveromyces lactis, Kluyveromyces waltii and Saccharomyces kluyveri, but the system is scaleable to accommodate additional genomes. This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at

Is attending lectures still relevant in engineering education?

A case study was conducted on a group of undergraduate chemical engineering students to assess the relevance of attending lectures from a student perspective and to understand why these students attend and do not attend lectures with a view to developing approaches to teaching, which are of greater interest and benefit to student learning. The students were surveyed by means of a questionnaire-type survey, which collected both quantitative and qualitative data from them. The majority of students stated that lectures are still very beneficial to their learning and are not an out-of-date mode of education. The major reasons for lecture non-attendance were time priority and curriculum overload issues with other scholarly activities and poor quality teaching. The students provided a number of suggestions to improve lectures and lecture attendance, including the incorporation of active learning in lectures, linking lectures to assessment and adding extra value to what is already in the notes

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, to infer the gene content and gene order that existed in the genome of an extinct ancestral yeast about 100 Mya, immediately before it underwent whole-genome duplication (WGD). The reconstructed ancestral genome contains 4,703 ordered loci on eight chromosomes. The reconstruction is complete except for the subtelomeric regions. We then inferred the series of rearrangement steps that led from this ancestor to the current Saccharomyces cerevisiae genome; relative to the ancestral genome we observe 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. Some fragile chromosomal sites were reused as evolutionary breakpoints multiple times. We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, including one that is derived from a hAT family transposon, and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD. Sites of gene gain and evolutionary breakpoints both tend to be associated with tRNA genes and, to a lesser extent, with origins of replication. Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources

Mechanisms of Chromosome Number Evolution in Yeast

The whole-genome duplication (WGD) that occurred during yeast evolution changed the basal number of chromosomes from 8 to 16. However, the number of chromosomes in post-WGD species now ranges between 10 and 16, and the number in non-WGD species (Zygosaccharomyces, Kluyveromyces, Lachancea, and Ashbya) ranges between 6 and 8. To study the mechanism by which chromosome number changes, we traced the ancestry of centromeres and telomeres in each species. We observe only two mechanisms by which the number of chromosomes has decreased, as indicated by the loss of a centromere. The most frequent mechanism, seen 8 times, is telomere-to-telomere fusion between two chromosomes with the concomitant death of one centromere. The other mechanism, seen once, involves the breakage of a chromosome at its centromere, followed by the fusion of the two arms to the telomeres of two other chromosomes. The only mechanism by which chromosome number has increased in these species is WGD. Translocations and inversions have cycled telomere locations, internalizing some previously telomeric genes and creating novel telomeric locations. Comparison of centromere structures shows that the length of the CDEII region is variable between species but uniform within species. We trace the complete rearrangement history of the Lachancea kluyveri genome since its common ancestor with Saccharomyces and propose that its exceptionally low level of rearrangement is a consequence of the loss of the non-homologous end joining (NHEJ) DNA repair pathway in this species

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

<p>Abstract</p> <p>Background</p> <p><it>Candida </it>species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of <it>Candida </it>genomic data. We have developed the <it>Candida </it>Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of <it>Candida </it>species. CGOB incorporates all available <it>Candida </it>clade genome sequences including two <it>Candida albicans </it>isolates (SC5314 and WO-1) and 8 closely related species (<it>Candida dubliniensis</it>, <it>Candida tropicalis</it>, <it>Candida parapsilosis</it>, <it>Lodderomyces elongisporus</it>, <it>Debaryomyces hansenii</it>, <it>Pichia stipitis</it>, <it>Candida guilliermondii </it>and <it>Candida lusitaniae</it>). <it>Saccharomyces cerevisiae </it>is also included as a reference genome.</p> <p>Results</p> <p>CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved <it>Candida </it>gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all <it>Candida </it>species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in <it>C. albicans</it>.</p> <p>Conclusions</p> <p>Our analysis provides an important resource that is now available for the <it>Candida </it>community. CGOB is available at <url>http://cgob.ucd.ie</url>.</p

Improved Performance of Near infrared Excitation Raman Spectroscopy Using Reflective Thin-film Gold on Glass Substrates for Cytology Samples

Confocal near-infrared Raman spectroscopy has been shown to have applications in the area of clinical biology. A source wavelength in the near infrared is preferred over visible wavelengths for inspecting biological samples due to superior wave number resolution and reduced photo damage. However, these excitation sources have a number of drawbacks when compared to lasers in the visible wavelength region, including the requirement to use expensive highly pure crystal substrates such as Raman grade calcium fluoride as well as long acquisition times due to the lower Raman scattering efficiency. This paper investigates the use of a reflective substrate comprising a low cost 100 nm thin-film gold on glass substrate, as an alternative. Similar to recent work that used stainless steel substrates, it is demonstrated that the thin-film gold coated substrates, which are relatively inexpensive, produce cell spectra with 1.65 times the signal to noise ratio when compared with spectra obtained from calcium fluoride under identical conditions, with no apparent background signal in the fingerprint region. Two prostate cell lines are examined having been deposited on glass, calcium fluoride, and thin-film gold on glass substrates using the Thin Prep standard. Background spectra from, and cell adhesion on, these three substrates are compared. A comparison of the intensities and signal to noise ratios of the resulting spectra, and their viability for classification using principle components analysis is performed, which further demonstrates the benefit of reflective substrates

Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH, and a fermentative metabolism with a fast growth rate. Here we used RNA-seq to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than in control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/2, previously described as lactic acid-responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii as compared to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production.Importance Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression in conditions of interest, and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains

Comparative genome analysis and gene finding in Candida species using CGOB.

The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data

Exploring perspectives on chronic obstructive pulmonary disease in people who smoke heroin: a qualitative study

Background Smoking rather than injecting heroin has become more common over the last twenty years. Although there is an increasing body of evidence describing high levels of COPD in heroin smokers, there is limited evidence documenting the impact this has on this population group. Aim. We aimed to describe the experiences of heroin smokers with COPD in Liverpool, UK Design and Setting Participants were purposefully sampled for this qualitative study. Participants included were adults enrolled in an opioid replacement clinic run by Addaction in Liverpool, UK and whom had already engaged with spirometry testing for COPD as part of a previous study Methods. We preformed semi-structured interviews with participants with spirometrically-confirmed COPD in opioid replacement clinics in Liverpool, UK. Data were analysed using a framework analysis approach. Results. We invited 16 potential participants of whom 10 agreed to take part and were interviewed. Three themes common to all interviews were identified: functional measures of lung health that impacted on their activities of daily living, inhaler and medication perceptions with erratic use that was not concordant with their prescription, and the impact of difficulties accessing care. Conclusion. These findings, along with previous studies highlighting the prevalence of COPD in this population, warrant efforts to integrate community COPD and opioid replacement services to improve outcomes for this vulnerable population