Recalibrated Tree of Leaf Beetles (Chrysomelidae) Indicates Independent Diversification of Angiosperms and Their Insect Herbivores

BACKGROUND: The great diversity of the “Phytophaga” (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion. METHODOLOGY: A phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini. PRINCIPAL FINDINGS: The origin of the Chrysomelidae was dated to 73–79 Mya (confidence interval 63–86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage. CONCLUSIONS: Previous calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly

Internet application for flexible learning of control engineering and robotics

This talk presents the development of a set of tele-robotic systems, funded by HEA Departmental TDG, to support control engineering and robotic courses. Technical details of the development will be presented. Experience working on this development will be shared, and outcome and impact of this development will also be discussed

Equine grass sickness (a multiple systems neuropathy) is associated with alterations in the gastrointestinal mycobiome

Background: Equine grass sickness (EGS) is a multiple systems neuropathy of grazing horses of unknown aetiology. An apparently identical disease occurs in cats, dogs, rabbits, hares, sheep, alpacas and llamas. Many of the risk factors for EGS are consistent with it being a pasture mycotoxicosis. To identify potential causal fungi, the gastrointestinal mycobiota of EGS horses were evaluated using targeted amplicon sequencing, and compared with those of two control groups. Samples were collected post mortem from up to 5 sites in the gastrointestinal tracts of EGS horses (EGS group; 150 samples from 54 horses) and from control horses that were not grazing EGS pastures and that had been euthanased for reasons other than neurologic and gastrointestinal diseases (CTRL group; 67 samples from 31 horses). Faecal samples were also collected from healthy control horses that were co-grazing pastures with EGS horses at disease onset (CoG group; 48 samples from 48 horses). Results: Mycobiota at all 5 gastrointestinal sites comprised large numbers of fungi exhibiting diverse taxonomy, growth morphology, trophic mode and ecological guild. FUNGuild analysis parsed most phylotypes as ingested environmental microfungi, agaricoids and yeasts, with only 1% as gastrointestinal adapted animal endosymbionts. Indices of alpha-diversity indicated that mycobiota richness and diversity varied throughout the gastrointestinal tract and were greater in EGS horses. There were significant inter-group and inter-site differences in mycobiota structure. A large number of phylotypes were differentially abundant among groups. Key phylotypes (n=56) associated with EGS were identified that had high abundance and high prevalence in EGS samples, significantly increased abundance in EGS samples, and were important determinants of the inter-group differences in mycobiota structure. Many key phylotypes were extremophiles and/or were predicted to produce cytotoxic and/or neurotoxic extrolites. Conclusions: This is the first reported molecular characterisation of the gastrointestinal mycobiota of grazing horses. Key phylotypes associated with EGS were identified. Further work is required to determine whether neurotoxic extrolites from key phylotypes contribute to EGS aetiology or whether the association of key phylotypes and EGS is a consequence of disease or is non-causal

Clinical measurements performed during alfaxalone total intravenous anaesthesia for radiography and neurophysiological investigations in dogs

Objective: To describe clinically relevant, physiological measurements collected during a 3- hour duration alfaxalone total intravenous anaesthesia.Study design: Case series.Animals: A total of 112 client-owned middle aged or older dogs.Methods: Dogs were premedicated with intramuscular acepromazine (0.03 mg kg-1). Anaesthesia was induced and subsequently maintained for up to 3 hours with alfaxalone administered intravenously. Dogs breathed 100% oxygen via an endotracheal tube. Heart rate, respiratory rate, and blood pressure were evaluated 30 minutes after administration of acepromazine and used as baseline values for comparisons of intra-anaesthetic data. Blood glucose was measured one week prior to anaesthesia and every hour during alfaxalone anaesthesia. Quality and duration of recovery were recorded. Mean data for physiological variables were compared over three time points; before induction of anaesthesia, forthe first hour of anaesthesia and from 60 minutes to discontinuation of anaesthesia.Results: Mean induction dose of alfaxalone was 1.4 (95% CI 1.3 - 1.5) mg kg-1. Post induction apnoea for greater than 60 seconds occurred in 13 (11.6%) dogs. Mean alfaxalone infusion rate during the first 60 minutes of anaesthesia was 0.099 mg kg-1 minute-1; from 60 minutes until discontinuation of anaesthesia, mean infusion rate was 0.092 mg kg-1 minute-1. Heart rate was well maintained; hypotension (mean arterial blood pressure less than 60 mmHg) was encountered in 23 (21%) of dogs. Blood glucose levels did not alter during anaesthesia. Median time between discontinuation of alfaxalone infusion and extubation was 17 (7 – 35 minutes), time to assuming sternal recumbency was 75 (58 - 110 minutes), and time to standing was 109 (88 - 140 minutes).Conclusions and clinical relevance: Alfaxalone infusion provided effective anaesthesia in this population. In a minority of cases respiratory and haemodynamic support of the patient was required

Expansion of the HSFY gene family in pig lineages : HSFY expansion in suids.

BACKGROUND: Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. The Y-linked heat shock transcription factor (HSFY) family has become amplified on the Y chromosome of the domestic pig (Sus scrofa), in an apparently independent event to an HSFY expansion on the Y chromosome of cattle (Bos taurus). Although the biological functions of HSFY genes are poorly understood, they appear to be involved in gametogenesis in a number of mammalian species, and, in cattle, HSFY gene copy number may correlate with levels of fertility. RESULTS: We have investigated the HSFY family in domestic pig, and other suid species including warthog, bushpig, babirusa and peccaries. The domestic pig contains at least two amplified variants of HSFY, distinguished predominantly by presence or absence of a SINE within the intron. Both these variants are expressed in testis, and both are present in approximately 50 copies each in a single cluster on the short arm of the Y. The longer form has multiple nonsense mutations rendering it likely non-functional, but many of the shorter forms still have coding potential. Other suid species also have these two variants of HSFY, and estimates of copy number suggest the HSFY family may have amplified independently twice during suid evolution. CONCLUSIONS: The HSFY genes have become amplified in multiple species lineages independently. HSFY is predominantly expressed in testis in domestic pig, a pattern conserved with cattle, in which HSFY may play a role in fertility. Further investigation of the potential associations of HSFY with fertility and testis development may be of agricultural interest.We gratefully acknowledge the Wellcome Trust Sanger Institute core teams for fingerprinting, mapping, archiving, library construction, sequence improvement and sequencing and Genus for providing the Duroc boar samples. This work was funded by BBSRC grant BB/F021372/1. The Flow Cytometry and Cytogenetics Core Facilities at the Wellcome Trust Sanger Institute and Sanger investigators are funded by the Wellcome Trust (grant number WT098051)

A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13).

BACKGROUND: Rhinovirus infection is a major cause of asthma exacerbations. OBJECTIVES: We studied nasal and bronchial mucosal inflammatory responses during experimental rhinovirus-induced asthma exacerbations. METHODS: We used nasosorption on days 0, 2-5 and 7 and bronchosorption at baseline and day 4 to sample mucosal lining fluid to investigate airway mucosal responses to rhinovirus infection in patients with allergic asthma (n=28) and healthy non-atopic controls (n=11), by using a synthetic absorptive matrix and measuring levels of 34 cytokines and chemokines using a sensitive multiplex assay. RESULTS: Following rhinovirus infection asthmatics developed more upper and lower respiratory symptoms and lower peak expiratory flows compared to controls (all P<0.05). Asthmatics also developed higher nasal lining fluid levels of an anti-viral pathway (including IFN-γ, IFN-λ/IL-29, CXCL11/ITAC, CXCL10/IP10 and IL-15) and a type 2 inflammatory pathway (IL-4, IL-5, IL-13, CCL17/TARC, CCL11/eotaxin, CCL26/eotaxin-3) (area under curve day 0-7, all P<0.05). Nasal IL-5 and IL-13 were higher in asthmatics at day 0 (P<0.01) and levels increased by days 3 and 4 (P<0.01). A hierarchical correlation matrix of 24 nasal lining fluid cytokine and chemokine levels over 7days demonstrated expression of distinct interferon-related and type 2 pathways in asthmatics. In asthmatics IFN-γ, CXCL10/IP10, CXCL11/ITAC, IL-15 and IL-5 increased in bronchial lining fluid following viral infection (all P<0.05). CONCLUSIONS: Precision sampling of mucosal lining fluid identifies robust interferon and type 2 responses in the upper and lower airways of asthmatics during an asthma exacerbation. Nasosorption and bronchosorption have potential to define asthma endotypes in stable disease and at exacerbation

The role of Havana and communities in the manual curation of unfinished vertebrate genomes

Manual annotation&#x202d; (&#x202c;the&#x202d; &#x22;&#x202c;museum&#x202d;&#x22; &#x202c;model of annotation&#x202d;) &#x202c;relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.&#x202d; This&#x202c; is both costly and time consuming and therefore is used only for model organisms with sufficient funding.&#x202d; &#x202c;Smaller research communities often have to rely on other models of annotation,&#x202d; &#x202c;mainly automated annotation&#x202d; (&#x202c;the&#x202d; &#x22;&#x202c;factory&#x202d;&#x22; &#x202c;model,&#x202d; &#x202c;e.g.&#x202d; &#x202c;Ensembl&#x202d;)&#x202c;,&#x202d; &#x202c;and the&#x202d; &#x22;&#x202c;jamboree&#x202d;&#x22; &#x202c;model&#x202d; (&#x202c;in which a group of leading biologists from the community and bioinformaticians come together for a short intensive annotation workshop&#x202d;)&#x202c;.&#x202d; &#x202c;At the Wellcome Trust Sanger Institute&#x202d; (&#x202c;WTSI&#x202d;)&#x202c;,&#x202d; &#x202c;the Havana team provides high quality manual annotation of finished vertebrate genome sequences,&#x202d; &#x202c;namely human,&#x202d; &#x202c;mouse and zebrafish.&#x202d; &#x202c;We also perform the curation of specific finished regions such as the MHC in dog,&#x202d; &#x202c;cow and pig,&#x202d; &#x202c;whose whole genomes have been&#x202d; &#x202c;assembled from unfinished BACs or from whole genome shotgun sequences.&#x202d; &#x202c;In addition,&#x202d; &#x202c;we at Havana have also hosted annotation jamborees for the cow&#x202d; (&#x202c;Bos taurus&#x202d;) &#x202c;and pig&#x202d; (&#x202c;Sus scrofa&#x202d;) &#x202c;genomes.&#x202d; &#x202c;During those sessions,&#x202d; &#x202c;the research community had the opportunity to annotate their genes of interest under expert guidance using the custom written publicly available Otterlace annotation system,&#x202d; &#x202c;and the unified manual annotation guidelines.&#x202d; &#x202c;By making use of the tools and skills acquired during the cow and pig jamborees,&#x202d; &#x202c;the delegates can continue annotating their genomes remotely.&#x202d; &#x202c;For the pig genome,&#x202d; &#x202c;a highly contiguous physical map has been generated by an international effort of four laboratories (available in Pre!Ensembl) and&#x202d; &#x202c;is being used as a substrate for the swine genome sequencing project.&#x202d; &#x202c;Upcoming vertebrate genomes will be sequenced to a high depth coverage with the next generation sequencing technologies&#x202d; (&#x202c;e.g.&#x202d; &#x202c;Illumina,&#x202d; &#x202c;454,&#x202d; &#x202c;SOLiD&#x202d;) &#x202c;but will have the drawback of not being manually finished.&#x202d; &#x202c;Manual annotation will be more accurate than the automated predictions at coping with any assembly problems derived from these high coverage but unfinished&#x202d; (&#x202c;or automatic pre-finished&#x202d;) &#x202c;genomes.&#x202d; &#x202c;Once these inherent assembly errors are corrected and the gene structures are accurately identified with manual annotation,&#x202d; &#x202c;the curated genes will be incorporated and merged with the predicted gene models in Ensembl to provide a unified view of the landscape of vertebrate genomes.&#x202d; &#x202c;I will present an introduction to our manual annotation system and our experience using it for annotation jamborees at the WTSI