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Bacteria evoke alarm behaviour in zebrafish

Suresh Jesuthasan, Joanne Chia, Karen Guillemin, Ruey-Kuang Cheng, Tom Rowland, Kathleen Cheow & Elena Wall
Confocal microscopy files and tracking data to accompany the paper.

SI: Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE: Molecular Dynamics Trajectories

Christof Jaeger
SI: Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE:
Truncated MD trajectories in pdb format

SI: Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE: Molecular Dynamics Trajectories

Christof Jaeger
SI: Radical Stabilization Energies for Enzyme Engineering – Tackling the Substrate Scope of the Radical Enzyme QueE:
Truncated MD trajectories in pdb format

GliderTools: A Python toolbox for processing underwater glider data

Luke Gregor, Thomas Ryan-Keogh, Sarah-Anne Nicholson, Marcel Du Plessis, Isabelle Giddy & Sebastiaan Swart
A toolkit for processing ocean diving glider data: despiking, smoothing, outlier detection, backscatter, fluorescence quenching, calibration, gridding, interpolation.
Documentation at https://glidertools.readthedocs.io

GliderTools: A Python toolbox for processing underwater glider data

Luke Gregor, Thomas Ryan-Keogh, Sarah-Anne Nicholson, Marcel Du Plessis, Isabelle Giddy & Sebastiaan Swart
A toolkit for processing ocean diving glider data: despiking, smoothing, outlier detection, backscatter, fluorescence quenching, calibration, gridding, interpolation.
Documentation at https://glidertools.readthedocs.io

Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection

Joseph A. Awuni, Alice Bianco, Otilia J. Dogbey, Alice Fusaro, Daniel T. Yingar, Annalisa Salviato, Patrick T. Ababio, Adelaide Milani, Francesco Bonfante & Isabella Monne
Between November 2017 and February 2018, Ghanaian poultry producers reported to animal health authorities a dramatic increase in mortality rate and a relevant drop in egg production in several layer hen farms. Laboratory investigations revealed that the farms had been infected by the H9N2 influenza subtype. Virological and molecular characterization of the viruses identified in Ghana is described here for the first time. Whole genome analysis showed that the viruses belong to the G1-lineage and...

Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection

Joseph A. Awuni, Alice Bianco, Otilia J. Dogbey, Alice Fusaro, Daniel T. Yingar, Annalisa Salviato, Patrick T. Ababio, Adelaide Milani, Francesco Bonfante & Isabella Monne
Between November 2017 and February 2018, Ghanaian poultry producers reported to animal health authorities a dramatic increase in mortality rate and a relevant drop in egg production in several layer hen farms. Laboratory investigations revealed that the farms had been infected by the H9N2 influenza subtype. Virological and molecular characterization of the viruses identified in Ghana is described here for the first time. Whole genome analysis showed that the viruses belong to the G1-lineage and...

Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

Penelope A. Steer-Cope, Jeanine R. Sandy, Denise O’Rourke, Peter C. Scott, Glenn F. Browning & Amir H. Noormohammadi
Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected...

Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection

Joseph A. Awuni, Alice Bianco, Otilia J. Dogbey, Alice Fusaro, Daniel T. Yingar, Annalisa Salviato, Patrick T. Ababio, Adelaide Milani, Francesco Bonfante & Isabella Monne
Between November 2017 and February 2018, Ghanaian poultry producers reported to animal health authorities a dramatic increase in mortality rate and a relevant drop in egg production in several layer hen farms. Laboratory investigations revealed that the farms had been infected by the H9N2 influenza subtype. Virological and molecular characterization of the viruses identified in Ghana is described here for the first time. Whole genome analysis showed that the viruses belong to the G1-lineage and...

A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses

David N. Phalen, Jessica Agius, Frederico F. Vaz, John-Sebastian Eden, Laura C. Setyo & Shannon Donahoe
A Bourke’s parrot (Neopsephotus bourkii) originating from an aviary in Australia, containing two species of parrots, five species of finch and a species of dove, was presented for necropsy. The Bourke’s parrot died from gastritis caused by Macrorhabdus ornithogaster, but also had an interstitial nephritis and ureteritis with adenovirus-like inclusion bodies within collecting duct epithelial cells. The adenovirus causing the lesions was shown to be Psittacine adenovirus-2 (PsAdV-2) using a PCR assay specific for adenoviruses...

Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

Penelope A. Steer-Cope, Jeanine R. Sandy, Denise O’Rourke, Peter C. Scott, Glenn F. Browning & Amir H. Noormohammadi
Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected...

A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses

David N. Phalen, Jessica Agius, Frederico F. Vaz, John-Sebastian Eden, Laura C. Setyo & Shannon Donahoe
A Bourke’s parrot (Neopsephotus bourkii) originating from an aviary in Australia, containing two species of parrots, five species of finch and a species of dove, was presented for necropsy. The Bourke’s parrot died from gastritis caused by Macrorhabdus ornithogaster, but also had an interstitial nephritis and ureteritis with adenovirus-like inclusion bodies within collecting duct epithelial cells. The adenovirus causing the lesions was shown to be Psittacine adenovirus-2 (PsAdV-2) using a PCR assay specific for adenoviruses...

Pathogenicity of fowl adenovirus (FAdV) serotype 4 strain SDJN in Taizhou geese

Zhipeng Wei, He Liu, Youjiang Diao, Xudong Li, Shuai Zhang, Bin Gao, Yi Tang, Jingdong Hu & Youxiang Diao
Hydropericardium hepatitis syndrome (HHS) is a fatal disease in chickens, mainly caused by fowl adenovirus serotype 4 (FAdV-4). Since June 2015, HHS has appeared in many provinces in China. The disease has spread from broilers to laying hens, breeders and Cherry Valley ducks, seriously endangering the health of the poultry industry in China. In July 2016, an infectious disease was noticed in a goose farm in Jinan, Shandong Province, China, and hydropericardium was the main...

Pathogenicity of fowl adenovirus (FAdV) serotype 4 strain SDJN in Taizhou geese

Zhipeng Wei, He Liu, Youjiang Diao, Xudong Li, Shuai Zhang, Bin Gao, Yi Tang, Jingdong Hu & Youxiang Diao
Hydropericardium hepatitis syndrome (HHS) is a fatal disease in chickens, mainly caused by fowl adenovirus serotype 4 (FAdV-4). Since June 2015, HHS has appeared in many provinces in China. The disease has spread from broilers to laying hens, breeders and Cherry Valley ducks, seriously endangering the health of the poultry industry in China. In July 2016, an infectious disease was noticed in a goose farm in Jinan, Shandong Province, China, and hydropericardium was the main...

A survey of a mixed species aviary provides new insights into the pathogenicity, diversity, evolution, host range, and distribution of psittacine and passerine adenoviruses

David N. Phalen, Jessica Agius, Frederico F. Vaz, John-Sebastian Eden, Laura C. Setyo & Shannon Donahoe
A Bourke’s parrot (Neopsephotus bourkii) originating from an aviary in Australia, containing two species of parrots, five species of finch and a species of dove, was presented for necropsy. The Bourke’s parrot died from gastritis caused by Macrorhabdus ornithogaster, but also had an interstitial nephritis and ureteritis with adenovirus-like inclusion bodies within collecting duct epithelial cells. The adenovirus causing the lesions was shown to be Psittacine adenovirus-2 (PsAdV-2) using a PCR assay specific for adenoviruses...

Vaccination with FAdV-8a induces protection against inclusion body hepatitis caused by homologous and heterologous strains

Penelope A. Steer-Cope, Jeanine R. Sandy, Denise O’Rourke, Peter C. Scott, Glenn F. Browning & Amir H. Noormohammadi
Fowl aviadenoviruses (FAdV) are important avian pathogens, responsible for several poultry diseases prevalent worldwide, including inclusion body hepatitis (IBH). FAdV intraspecies cross-protection has been clearly demonstrated, but there is little evidence that any interspecies cross-protection exists. The present study aimed to assess the inter- and intraspecies protection between three FAdV field isolates (FAdV-8a, FAdV-8b, FAdV-11) identified in association with severe IBH outbreaks. Inocula prepared using inactivated plaque-purified virus with adjuvant Montanide™ ISA 71VG, were injected...

Investigation of suspected Newcastle disease (ND) outbreaks in Egypt uncovers a high virus velogenic ND virus burden in small-scale holdings and the presence of multiple pathogens

Ibrahim Moharam, Alaa Abd El Razik, Hesham Sultan, Mohammed Ghezlan, Clement Meseko, Kati Franzke, Timm Harder, Martin Beer & Christian Grund
Highly contagious Newcastle disease (ND) is associated with devastating outbreaks with highly variable clinical signs among gallinaceous birds. In this study we aimed to verify clinical ND suspicions in poultry holdings in Egypt suffering from respiratory distress and elevated mortality, comparing two groups of ND-vaccinated poultry holdings in three governorates. Besides testing for Newcastle disease virus (NDV), samples were screened for infectious bronchitis virus (IBV) and avian influenza virus (AIV) by RT-qPCR as well as...

Investigation of suspected Newcastle disease (ND) outbreaks in Egypt uncovers a high virus velogenic ND virus burden in small-scale holdings and the presence of multiple pathogens

Ibrahim Moharam, Alaa Abd El Razik, Hesham Sultan, Mohammed Ghezlan, Clement Meseko, Kati Franzke, Timm Harder, Martin Beer & Christian Grund
Highly contagious Newcastle disease (ND) is associated with devastating outbreaks with highly variable clinical signs among gallinaceous birds. In this study we aimed to verify clinical ND suspicions in poultry holdings in Egypt suffering from respiratory distress and elevated mortality, comparing two groups of ND-vaccinated poultry holdings in three governorates. Besides testing for Newcastle disease virus (NDV), samples were screened for infectious bronchitis virus (IBV) and avian influenza virus (AIV) by RT-qPCR as well as...

Broad-spectrum antimicrobial activity of volatile organic compounds from endophytic Pseudomonas putida BP25 against diverse plant pathogens

Valiya Nadakkakath Agisha, Aundy Kumar, Santhosh Joseph Eapen, Neelam Sheoran & Rajamma Suseelabhai
Black pepper endophytic Pseudomonas putida BP25 produced diverse antimicrobial volatile organic compounds having potential for plant disease management. Chemically synthesised volatiles such as 2, 5-dimethyl pyrazine; 2-methyl pyrazine; dimethyl trisulphide; 2-ethyl 5-methyl pyrazine; and 2-ethyl 3, 6-dimethyl pyrazine showed inhibitory activity against oomycete pathogens, Phytophthora capsici & Pythium myriotylum; fungal pathogens, Rhizoctonia solani, Colletotrichum gloeosporioides, Athelia rolfsii, Gibberella moniliformis & Magnaporthe oryzae; bacterial pathogen, Ralstonia pseudosolanacearum and plant parasitic nematode, Radopholus similis. Among them, dimethyl...

Broad-spectrum antimicrobial activity of volatile organic compounds from endophytic Pseudomonas putida BP25 against diverse plant pathogens

Valiya Nadakkakath Agisha, Aundy Kumar, Santhosh Joseph Eapen, Neelam Sheoran & Rajamma Suseelabhai
Black pepper endophytic Pseudomonas putida BP25 produced diverse antimicrobial volatile organic compounds having potential for plant disease management. Chemically synthesised volatiles such as 2, 5-dimethyl pyrazine; 2-methyl pyrazine; dimethyl trisulphide; 2-ethyl 5-methyl pyrazine; and 2-ethyl 3, 6-dimethyl pyrazine showed inhibitory activity against oomycete pathogens, Phytophthora capsici & Pythium myriotylum; fungal pathogens, Rhizoctonia solani, Colletotrichum gloeosporioides, Athelia rolfsii, Gibberella moniliformis & Magnaporthe oryzae; bacterial pathogen, Ralstonia pseudosolanacearum and plant parasitic nematode, Radopholus similis. Among them, dimethyl...

Raw data for Eacock et al (2019) Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception

Amy Eacock
Raw data for Eacock et al (2019) Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception.

Raw data for Eacock et al (2019) Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception

Amy Eacock
Raw data for Eacock et al (2019) Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception.

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Andrew Gichira, Sheila Avoga, Zhizhong Li, Guangwan Hu, Qingfeng Wang & Jinming Chen
Abstract Background Majority of the species within Senecioneae are classified in Senecio, making it the tribe’s largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its...

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Andrew Gichira, Sheila Avoga, Zhizhong Li, Guangwan Hu, Qingfeng Wang & Jinming Chen
Abstract Background Majority of the species within Senecioneae are classified in Senecio, making it the tribe’s largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its...

MOESM3 of Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

Andrew Gichira, Sheila Avoga, Zhizhong Li, Guangwan Hu, Qingfeng Wang & Jinming Chen
Additional file 3: Table S3. Number and type of microsatellite repeat motifs in each of the 11 complete chloroplast genomes.

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