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710,465 Works

Supplementary material from "Strong social relationships are associated with decreased longevity in a facultatively social mammal"

Daniel T. Blumstein, Dana M. Williams, Alexandra N. Lim, Svenja Kroeger & Julien G.A. Martin
Humans in strong social relationships are more likely to live longer because social relationships may buffer stressors and thus have protective effects. However, a shortcoming of human studies is that they often rely on self-reporting of these relationships. By contrast, observational studies of non-human animals permit detailed analyses of the specific nature of social relationships. Thus, discoveries that some social animals live longer and healthier lives if they are involved in social grooming, forage together...

Mechanochemically-generated solid state complex of C60-fullerene with tetra-(5,7-diphenyl)calix[4]azulene, NMR, XRD and DFT studies

Celine Schneider, Hidetaka Nishimura, Jaehyun Lee, Lawrence T. Scott, Atsushi Wakamiya, Roy Forbes & Paris E. Georghiou
The synthesis of tetra-(5,7-diphenyl)calix[4]azulene via the reaction of 5,7-diphenylazulene with formaldehyde is described. Its solid-state supramolecular complexation with C60 produced by a grinding of the two components was evaluated by solid-state 13C-NMR spectroscopy and X-ray powder diffraction. Gas-phase DFT studies of possible structures are reported.

Additional file 2: of Myocardial inflammation, injury and infarction during on-pump coronary artery bypass graft surgery

Shirjel Alam, Colin Stirrat, Nick Spath, Vipin Zamvar, Renzo Pessotto, Marc Dweck, Colin Moore, Scott Semple, Ahmed El-Medany, Divya Manoharan, Nicholas Mills, Anoop Shah, Saeed Mirsadraee, David Newby & Peter Henriksen
Correlations and change in ejection fraction (pre to post surgery). (DOCX 176 kb)

Myocardial inflammation, injury and infarction during on-pump coronary artery bypass graft surgery

Shirjel Alam, Colin Stirrat, Nick Spath, Vipin Zamvar, Renzo Pessotto, Marc Dweck, Colin Moore, Scott Semple, Ahmed El-Medany, Divya Manoharan, Nicholas Mills, Anoop Shah, Saeed Mirsadraee, David Newby & Peter Henriksen
Abstract Background Myocardial inflammation and injury occur during coronary artery bypass graft (CABG) surgery. We aimed to characterise these processes during routine CABG surgery to inform the diagnosis of type 5 myocardial infarction. Methods We assessed 87 patients with stable coronary artery disease who underwent elective CABG surgery. Myocardial inflammation, injury and infarction were assessed using plasma inflammatory biomarkers, high-sensitivity cardiac troponin I (hs-cTnI) and cardiac magnetic resonance imaging (CMR) using both late gadolinium enhancement...

Myocardial inflammation, injury and infarction during on-pump coronary artery bypass graft surgery

Shirjel Alam, Colin Stirrat, Nick Spath, Vipin Zamvar, Renzo Pessotto, Marc Dweck, Colin Moore, Scott Semple, Ahmed El-Medany, Divya Manoharan, Nicholas Mills, Anoop Shah, Saeed Mirsadraee, David Newby & Peter Henriksen
Abstract Background Myocardial inflammation and injury occur during coronary artery bypass graft (CABG) surgery. We aimed to characterise these processes during routine CABG surgery to inform the diagnosis of type 5 myocardial infarction. Methods We assessed 87 patients with stable coronary artery disease who underwent elective CABG surgery. Myocardial inflammation, injury and infarction were assessed using plasma inflammatory biomarkers, high-sensitivity cardiac troponin I (hs-cTnI) and cardiac magnetic resonance imaging (CMR) using both late gadolinium enhancement...

Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
Abstract Background Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long-...

Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
Abstract Background Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long-...

Additional file 9: of Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
Phylogenetic tree of DHPS proteins encoded by chromosomal genes and mobile sulfonamide resistance genes. (TXT 283 kb)

Additional file 1: of Myocardial inflammation, injury and infarction during on-pump coronary artery bypass graft surgery

Shirjel Alam, Colin Stirrat, Nick Spath, Vipin Zamvar, Renzo Pessotto, Marc Dweck, Colin Moore, Scott Semple, Ahmed El-Medany, Divya Manoharan, Nicholas Mills, Anoop Shah, Saeed Mirsadraee, David Newby & Peter Henriksen
Systemic inflammatory markers. (DOCX 387 kb)

Additional file 8: of Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
Phylogenetic tree of the identified OXA-variant gene cassettes and 289 known OXA-variants retrieved from the CARD database. (TXT 9 kb)

DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Thomas Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen Davis, Russell Snell, Richard Spelman & Mathew Littlejohn
Abstract Background Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits. Results Using a discovery population of 12,000 taurine dairy cattle, we detail 27...

DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Thomas Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen Davis, Russell Snell, Richard Spelman & Mathew Littlejohn
Abstract Background Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits. Results Using a discovery population of 12,000 taurine dairy cattle, we detail 27...

Canary: an atomic pipeline for clinical amplicon assays

Kenneth Doig, Jason Ellul, Andrew Fellowes, Ella Thompson, Georgina Ryland, Piers Blombery, Anthony Papenfuss & Stephen Fox
Abstract Background High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of...

Canary: an atomic pipeline for clinical amplicon assays

Kenneth Doig, Jason Ellul, Andrew Fellowes, Ella Thompson, Georgina Ryland, Piers Blombery, Anthony Papenfuss & Stephen Fox
Abstract Background High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of...

Additional file 6 of DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Thomas Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen Davis, Russell Snell, Richard Spelman & Mathew Littlejohn
Figure S3. WGS resolution for eQTL of all gene located within 1Mbp windows centred on QTL peaks for lactose phenotypes. (PDF 8428 kb)

Additional file 7: of Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
Protein sequences of the synthesized genes in fasta format. (TXT 1 kb)

Additional file 1: of Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex

Gina Conte, Kathryn Hodgins, Sam Yeaman, Jon Degner, Sally Aitken, Loren Rieseberg & Michael Whitlock
Supplementary Material. Supplementary Figure S1-S6 (referenced in text). (PDF 9957 kb)

Additional file 3: File 3. of Canary: an atomic pipeline for clinical amplicon assays

Kenneth Doig, Jason Ellul, Andrew Fellowes, Ella Thompson, Georgina Ryland, Piers Blombery, Anthony Papenfuss & Stephen Fox
Example Pipeline Commands.txt: Validation pipeline command examples. (TXT 6 kb)

Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex

Gina Conte, Kathryn Hodgins, Sam Yeaman, Jon Degner, Sally Aitken, Loren Rieseberg & Michael Whitlock
Abstract Background Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit...

Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex

Gina Conte, Kathryn Hodgins, Sam Yeaman, Jon Degner, Sally Aitken, Loren Rieseberg & Michael Whitlock
Abstract Background Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit...

Additional file 2: Table S1. of Canary: an atomic pipeline for clinical amplicon assays

Kenneth Doig, Jason Ellul, Andrew Fellowes, Ella Thompson, Georgina Ryland, Piers Blombery, Anthony Papenfuss & Stephen Fox
xlsx: Comparison statistics for Canary, BWA, GATK and VarDict. (XLSX 45 kb)

Additional file 6: of Discovery of the fourth mobile sulfonamide resistance gene

Mohammad Razavi, Nachiket Marathe, Michael Gillings, Carl-Fredrik Flach, Erik Kristiansson & D. Joakim Larsson
List of metagenomic samples searched for sul4 genes. (XLSX 376 kb)

Additional file 5 of DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Thomas Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen Davis, Russell Snell, Richard Spelman & Mathew Littlejohn
Table S1. All genes used in the functional annotation clusters pathway analysis tool (DAVID), along with the output clusters and associated enrichment scores and enriched annotation classes. (XLSX 41 kb)

Training the salmon’s genes: influence of aerobic exercise, swimming performance and selection on gene expression in Atlantic salmon

Nicholas Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle & Aleksei Krasnov
Abstract Background Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and...

Training the salmon’s genes: influence of aerobic exercise, swimming performance and selection on gene expression in Atlantic salmon

Nicholas Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle & Aleksei Krasnov
Abstract Background Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and...

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