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Statistical supplement to: Biomechanics of the peafowl’s crest: a potential mechanosensory role for feathers during social displays

Roslyn Dakin, Daniel Van Beveren & Suzanne Amador Kane
Data and figures on peafowl crest feather vibration and mechanical properties. This fileset includes the data, R scripts, and figure files necessary to reproduce the figures and analysis.

Supplementary material from "Corals hosting symbiotic hydrozoans are less susceptible to predation and disease"

Simone Montano, Simone Fattorini, Valeriano Parravicini, Michael L. Berumen, Paolo Galli, Davide Maggioni, Roberto Arrigoni, Davide Seveso & Giovanni Strona
In spite of growing evidence that climate change may dramatically affect networks of interacting species, whether—and to what extent—ecological interactions can mediate species' response to disturbances is an open question. Here we show how a largely overseen association such as that between hydrozoans and scleractinian corals could be possibly associated with a reduction in coral susceptibility to ever-increasing predator and disease outbreaks. We examined 2450 scleractinian colonies (from both Maldivian and the Saudi Arabian coral...

Supplementary material from "Atlantic bluefin tuna spawn at suboptimal temperatures for their offspring"

P. Reglero, A. Ortega, R. Balbín, F.J. Abascal, A. Medina, E. Blanco, F. De La Gándara, D. Alvarez-Berastegui, M. Hidalgo, L. Rasmuson, F. Alemany & Ø. Fiksen
Life-history traits such as spawning migrations and timing of reproduction are adaptations to specific environmental constraints and seasonal cycles in many organisms' annual routines. In this study we analyse how offspring fitness constrains spawning phenology in a large migratory apex predator, the Atlantic bluefin tuna. The reproductive schedule of Atlantic bluefin tuna varies between spawning sites suggesting plasticity to local environmental conditions. Generally, temperature is considered to be the main constraint on tuna spawning phenology....

Supplementary material from "Atlantic bluefin tuna spawn at suboptimal temperatures for their offspring"

P. Reglero, A. Ortega, R. Balbín, F.J. Abascal, A. Medina, E. Blanco, F. De La Gándara, D. Alvarez-Berastegui, M. Hidalgo, L. Rasmuson, F. Alemany & Ø. Fiksen
Life-history traits such as spawning migrations and timing of reproduction are adaptations to specific environmental constraints and seasonal cycles in many organisms' annual routines. In this study we analyse how offspring fitness constrains spawning phenology in a large migratory apex predator, the Atlantic bluefin tuna. The reproductive schedule of Atlantic bluefin tuna varies between spawning sites suggesting plasticity to local environmental conditions. Generally, temperature is considered to be the main constraint on tuna spawning phenology....

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...

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...

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-...

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...

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...

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...

Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC)

Weilin Pu, Chenji Wang, Sidi Chen, Dunmei Zhao, Yinghui Zhou, Yanyun Ma, Ying Wang, Caihua Li, Zebin Huang, Li Jin, Shicheng Guo, Jiucun Wang & Minghua Wang
Abstract Background DNA methylation has been implicated as a promising biomarker for precise cancer diagnosis. However, limited DNA methylation-based biomarkers have been described in esophageal squamous cell carcinoma (ESCC). Methods A high-throughput DNA methylation dataset (100 samples) of ESCC from The Cancer Genome Atlas (TCGA) project was analyzed and validated along with another independent dataset (12 samples) from the Gene Expression Omnibus (GEO) database. The methylation status of peripheral blood mononuclear cells and peripheral blood...

Perceived Medical School stress of undergraduate medical students predicts academic performance: an observational study

Thomas Kötter, Josefin Wagner, Linda Brüheim & Edgar Voltmer
Abstract Background Medical students are exposed to high amounts of stress. Stress and poor academic performance can become part of a vicious circle. In order to counteract this circularity, it seems important to better understand the relationship between stress and performance during medical education. The most widespread stress questionnaire designed for use in Medical School is the “Perceived Medical School Stress Instrument” (PMSS). It addresses a wide range of stressors, including workload, competition, social isolation...

Perceived Medical School stress of undergraduate medical students predicts academic performance: an observational study

Thomas Kötter, Josefin Wagner, Linda Brüheim & Edgar Voltmer
Abstract Background Medical students are exposed to high amounts of stress. Stress and poor academic performance can become part of a vicious circle. In order to counteract this circularity, it seems important to better understand the relationship between stress and performance during medical education. The most widespread stress questionnaire designed for use in Medical School is the “Perceived Medical School Stress Instrument” (PMSS). It addresses a wide range of stressors, including workload, competition, social isolation...

Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC)

Weilin Pu, Chenji Wang, Sidi Chen, Dunmei Zhao, Yinghui Zhou, Yanyun Ma, Ying Wang, Caihua Li, Zebin Huang, Li Jin, Shicheng Guo, Jiucun Wang & Minghua Wang
Abstract Background DNA methylation has been implicated as a promising biomarker for precise cancer diagnosis. However, limited DNA methylation-based biomarkers have been described in esophageal squamous cell carcinoma (ESCC). Methods A high-throughput DNA methylation dataset (100 samples) of ESCC from The Cancer Genome Atlas (TCGA) project was analyzed and validated along with another independent dataset (12 samples) from the Gene Expression Omnibus (GEO) database. The methylation status of peripheral blood mononuclear cells and peripheral blood...

Mechanically tuned 3 dimensional hydrogels support human mammary fibroblast growth and viability

Kathryn Woods, Catlyn Thigpen, Jennifer Wang, Hana Park & Abigail Hielscher
Abstract Background Carcinoma associated fibroblasts (CAFs or myofibroblasts) are activated fibroblasts which participate in breast tumor growth, angiogenesis, invasion, metastasis and therapy resistance. As such, recent efforts have been directed toward understanding the factors responsible for activation of the phenotype. In this study, we have investigated how changes in the mechanical stiffness of a 3D hydrogel alter the behavior and myofibroblast-like properties of human mammary fibroblasts (HMFs). Results Here, we utilized microbial transglutaminase (mTG) to...

Mechanically tuned 3 dimensional hydrogels support human mammary fibroblast growth and viability

Kathryn Woods, Catlyn Thigpen, Jennifer Wang, Hana Park & Abigail Hielscher
Abstract Background Carcinoma associated fibroblasts (CAFs or myofibroblasts) are activated fibroblasts which participate in breast tumor growth, angiogenesis, invasion, metastasis and therapy resistance. As such, recent efforts have been directed toward understanding the factors responsible for activation of the phenotype. In this study, we have investigated how changes in the mechanical stiffness of a 3D hydrogel alter the behavior and myofibroblast-like properties of human mammary fibroblasts (HMFs). Results Here, we utilized microbial transglutaminase (mTG) to...

Spontaneous and CRISPR/Cas9-induced mutation of the osmosensor histidine kinase of the canola pathogen Leptosphaeria maculans

Alexander Idnurm, Andrew Urquhart, Dinesh Vummadi, Steven Chang, Angela Wouw & Francisco Lรณpez-Ruiz
Abstract Background The dicarboximide fungicide iprodione has been used to combat blackleg disease of canola (Brassica napus), caused by the fungus Leptosphaeria maculans. For example, in Australia the fungicide was used in the late 1990s but is no longer registered for use against blackleg disease, and therefore the impact of iprodione on L. maculans has not been investigated. Results Resistance to iprodione emerged spontaneously under in vitro conditions at high frequency. A basis for this...

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