Novel bioassays to examine the host-finding ability of plant-parasitic nematodes

We present two novel bioassays to be used in the examination of plant-parasitic nematode host-finding ability. The host-finding 'pipette-bulb assay' was constructed from modelled Pasteur pipette bulbs and connecting barrels using parafilm fastenings. This assay examines the direction of second-stage juvenile (J2) migration in response to a host seedling, through a moistened sand substrate, which underlies terminal upward-facing 'seedling bulbs', one containing a host seedling in potting compost, the other with only potting compost. An equal watering regime through both upward-facing seedling bulbs creates a directional concentration gradient of host diffusate chemotactic factors. Positive chemotactic stimuli cause the J2 to orientate and migrate towards the host plant. We present validation data collected from assays of the root-knot nematode, Meloidogyne incognita, and the potato cyst nematode, Globodera pallida, which indicate a highly significant positive attraction of J2 of both species to respective host plants. This represents a simple, quick and inexpensive method of assessing host-finding behaviour in the laboratory. We consider that the pipette-bulb assay improves on previous host-finding/chemo-attraction assays through creating a more biologically relevant environment for experimental J2; analysis is quick and easy, allowing the straightforward interpretation of results. In addition, we have developed an 'agar trough' sensory assay variant which we believe can be used rapidly to ratify nematode responses to chemical gustatory or olfactory cues. This was constructed from a water agar substrate such that two counting wells were connected by a raised central trough, all flooded with water. Two small water agar plugs were dehydrated briefly in an oven and then hydrated in either an attractant, repellent or water control; these plugs were then placed in the terminal counting wells and subsequently leached the attractant or repellent to form a concentration gradient along the central trough, which contained the initial J2 innoculum. Our data show that both M. incognita and G. pallida J2 are positively attracted to host diffusates. In addition, they displayed a strong repulsion in response to 1 M NaCl2. J2 of M. incognita displayed a mild aversion to a non-host oak root diffusate, whereas G. pallida J2 displayed a strong aversion to the same non-host diffusate; neither species responded to a compost leachate. We believe that the agar trough assay improves on previous methods by facilitating rapid diffusion of attractant or repellents. Both of the aforementioned assays were designed as tools to assess the impact of RNAi-based reverse genetics screens for gene targets involved in chemosensory orientation.

Genetic renal abnormalities

Inherited disorders of renal structure and function are relatively common causes of end-stage renal disease requiring renal replacement therapy. A family history of haematuria, urinary tract infection or renal failure can alert the clinician to the possible diagnosis of underlying renal genetic abnormalities. In practice, the commonest inherited renal disorder is autosomal dominant polycystic kidney disease (ADPKD), characterized by multiple kidney cysts associated with hypertension and renal failure. Insights into the cell biology of ADPKD are informing new therapeutic approaches to limit cyst growth and prevent progressive renal failure. Non-visible haematuria is a clinical finding that presents a diagnostic challenge because it has so many possible causes. Mutations in the genes encoding collagen proteins within the glomerular basement membrane (GBM) can disrupt its normal barrier function. Thin basement membrane nephropathy, caused by GBM collagen gene mutations, is a relatively common cause of familial haematuria that normally has a good long-term prognosis. Alport syndrome is a rare and genetically heterogeneous condition leading to renal failure in men inheriting the X-linked gene defect. Single-gene defects may cause diverse renal tubular disorders, such as predisposition to renal calculi, diabetes insipidus, renal tubular acidosis or hypertension with associated electrolyte imbalance. Gene mutations responsible for familial renal cancer syndromes, such as tuberous sclerosis complex and von Hippel–Lindau disease, have also been identified

flp-32 Ligand/Receptor Silencing Phenocopy Faster Plant Pathogenic Nematodes

Restrictions on nematicide usage underscore the need for novel control strategies for plant pathogenic nematodes such as Globodera pallida (potato cyst nematode) that impose a significant economic burden on plant cultivation activities. The nematode neuropeptide signalling system is an attractive resource for novel control targets as it plays a critical role in sensory and motor functions. The FMRFamide-like peptides (FLPs) form the largest and most diverse family of neuropeptides in invertebrates, and are structurally conserved across nematode species, highlighting the utility of the FLPergic system as a broad-spectrum control target. flp-32 is expressed widely across nematode species. This study investigates the role of flp-32 in G. pallida and shows that: (i) Gp-flp-32 encodes the peptide AMRNALVRFamide; (ii) Gp-flp-32 is expressed in the brain and ventral nerve cord of G. pallida; (iii) migration rate increases in Gp-flp-32-silenced worms; (iv) the ability of G. pallida to infect potato plant root systems is enhanced in Gp-flp-32-silenced worms; (v) a novel putative Gp-flp-32 receptor (Gp-flp-32R) is expressed in G. pallida; and, (vi) Gp-flp-32R silenced worms also display an increase in migration rate. This work demonstrates that Gp30 flp-32 plays an intrinsic role in the modulation of locomotory behaviour in G. pallida, and putatively interacts with at least one novel G-protein coupled receptor (Gp-flp-32R). This is the first functional characterisation of a parasitic nematode FLP-GPCR. © 2013 Atkinson et al.

Iris cysts in children:Classification, incidence, and management. The 1998 Torrence A Makley Jr Lecture

Background - Iris cysts in children are uncommon and there is relatively little information on their classification, incidence, and management. Methods - The records of all children under age 20 years who were diagnosed with iris cyst were reviewed and the types and incidence of iris cysts of childhood determined. Based on these observations recommendations were made regarding management of iris cysts in children. Results - Of 57 iris cysts in children, 53 were primary and four were secondary. There were 44 primary cysts of the iris pigment epithelium, 34 of which were of the peripheral or iridociliary type, accounting for 59% of all childhood iris cysts. It was most commonly diagnosed in the teenage years, more common in girls (68%), was not recognised in infancy, remained stationary or regressed, and required no treatment. The five mid-zonal pigment epithelial cysts were diagnosed at a mean age of 14 years, were more common in boys (83%), remained stationary, and required no treatment. The pupillary type of pigment epithelial cyst was generally recognised in infancy and, despite involvement of the pupillary aperture, also required no treatment. There were nine cases of primary iris stromal cysts, accounting for 16% of all childhood iris cysts. This cyst was usually diagnosed in infancy, was generally progressive, and required treatment in eight of the nine cases, usually by aspiration and cryotherapy or surgical resection. Among the secondary iris cysts, two were post-traumatic epithelial ingrowth cysts and two were tumour induced cysts, one arising from an intraocular lacrimal gland choristoma and one adjacent to a peripheral iris naevus. Conclusions - Most iris cysts of childhood are primary pigment epithelial cysts and require no treatment. However, the iris stromal cyst, usually recognised in infancy, is generally an aggressive lesion that requires treatment by aspiration or surgical excision.

Cavitary melanoma of the ciliary body. A study of eight cases

Purpose: The authors present the unique clinical features of cavitary uveal melanoma. Design: Retrospective chart review. Participants: Eight patients with cavitary uveal melanoma. Main Outcome Measures: The clinical, ultrasonographic, and histopathologic features of eight patients with cavitary melanoma of the ciliary body were studied. Results: In all eyes there was a brown ciliary body mass that blocked transmission of light on trans-scleral transillumination. Ocular ultrasonography revealed a large, single hollow cavity (unilocular 'pseudocyst') in five cases and multiple hollow cavities (multilocular 'pseudocyst') in three cases. The cavity occupied a mean of 55% of the entire mass thickness (range, 31%-79%). In five cases, a basal uveal mass was noted on ultrasonography. Four patients underwent tumor resection; one had enucleation, and three had 1251 radioactive plaque treatment. In the five cases confirmed histopathologically, the cavitation was empty, contained erythrocytes, serous fluid, and/or pigment-laden macrophages. In no case was the cavity lined by necrotic tumor, endothelial cells, or epithelial cells. Conclusion: Ciliary body melanoma can develop an intralesional cavity resembling an intraocular cyst. The presence of a solid mass at the base and a thick wall surrounding the cavity can assist in the differentiation of cavitary melanoma from benign cyst.

Foveal relocation by redistribution of the neurosensory retina

Aim - To describe a new surgical technique for foveal relocation, and to report the outcome in nine patients treated with this procedure. Methods - Nine consecutive patients with subfoveal choroidal neovascular membranes (CNVMs) secondary to age related macular degeneration underwent foveal relocation surgery by redistribution of the neurosensory retina (RNR). The technique involved induction of a retinal detachment via a single retinotomy, relocation of the fovea by 'sweeping' the retinal tissue with a retinal brush, and stabilisation of the retina in its new location using perfluorocarbon liquid peroperatively and silicone oil postoperatively. Results - In eight of nine eyes successful relocation of the fovea was achieved; in one eye the CNVM remained in a subfoveal location postoperatively. Visual acuity improved in two eyes, remained unchanged in three, and decreased in four eyes after a median follow up of 4 months (range 2.5-6 months). Complications included rupture of a foveal cyst with the development of a macular hole in one eye and epimacular membrane formation in another eye. In two eyes, macular retinal vessel closure occurred at the time of laser photocoagulation; one of these eyes later developed cystoid macular oedema and the other an epiretinal membrane. Recurrence of the CNVM was observed in one eye, but was controlled with further laser treatment. Conclusions - Foveal relocation by RNR appears to be feasible, obviating the need for extensive retinotomies or scleral shortening.

Tolvaptan in patients with autosomal dominant polycystic kidney disease

The course of autosomal dominant polycystic kidney disease (ADPKD) is often associated with pain, hypertension, and kidney failure. Preclinical studies indicated that vasopressin V(2)-receptor antagonists inhibit cyst growth and slow the decline of kidney function.

Prosthodontic rehabilitation of a patient using a swing-lock lower denture after segmental mandibulectomy

A swing-lock denture is useful in partially dentate patients where the configuration of the remaining teeth means that either the retention or stability available for a conventional removable partial denture is compromised. Such removable prostheses can also prove to be extremely useful when providing prosthodontic rehabilitation following surgical resection of oral cancer. A 20 year-old patient was referred to the Restorative Department of Cork University Dental Hospital following segmental mandibulectomy to treat a calicifying epithelial odontogenic tumour (Pindborg Tumour). Initial treatment using a conventional lower partial denture failed. This paper outlines the successfully rehabilitation using a lower Cobalt-Chromium swing-lock partial denture.

John Birks: Pioneer in quantitative palaeoecology

We describe the career of John Birks as a pioneering scientist who has, over a career spanning five decades, transformed palaeoecology from a largely descriptive to a rigorous quantitative science relevant to contemporary questions in ecology and environmental change. We review his influence on students and colleagues not only at Cambridge and Bergen Universities, his places of primary employment, but also on individuals and research groups in Europe and North America. We also introduce the collection of papers that we have assembled in his honour. The papers are written by his former students and close colleagues and span many of the areas of palaeoecology to which John himself has made major contributions. These include the relationship between ecology and palaeoecology, late-glacial and Holocene palaeoecology, ecological succession, climate change and vegetation history, the role of palaeoecological techniques in reconstructing and understanding the impact of human activity on terrestrial and freshwater ecosystems and numerical analysis of multivariate palaeoecological data.

A multi-proxy chronological reconstruction of palaeosalinity in the eastern Limfjord, Denmark

The Jutland peninsula in northern Denmark is home to the Limfjord, one of the largest estuarine bodies of water in the region. Human inhabitance of the Limfjord’s surrounding coastlines stretches back further than 7,800 cal BP, with anthropogenic influence on the landscape beginning approximately 6,000 cal BP. Understanding how the Limfjord as a system has changed throughout time is useful in comprehending subsistence patterns and anthropogenic influence. This research is part of a larger project aimed at discerning subsistence patterns and environmental change in the region. Following the Younger Dryas, as the Fennoscandian ice sheet began to melt, Denmark experienced isostatic rebound, which contributed to the complex sea level history in the region. Between ice melt and isostatic rebound, the Jutland peninsula experienced many transgression and regression events. Connections to surrounding seas have shifted throughout time, with most attention focused on the western connection of the Limfjord with the North Sea, which has experienced numerous closures and subsequent re-openings throughout the Holocene. Furthermore, the Limfjord-North Sea connection has been the focal point of research because of the west to east water flow in the system, and the present day higher salinity in the west compared to the east. Little to no consideration has been paid to the influence of the Kattegat and Baltic on the Limfjord until now. A 10m sediment core was taken from Sebbersund (near Nibe, Limfjord), along the connection between the Limfjord and the Kattegat in the east to understand how the eastern part of the system has changed and differed from changes observed in the west. The Sebbersund sequence spans a majority of the Holocene, from 9600 cal BP to 1030 cal BP, determined via radiocarbon dating of terrestrial macrofossils and bulk sediment. Over this time period palaeoenvironmental conditions were reconstructed through the use of geochemical analyses (13C, 15N, C:N), physical sediment analyses, dinoflagellate cyst abundances and molluscan analyses. apart from two instances of low salinity, one at the top and one at the bottom of the core, the sequence has a strong marine signal for a majority of the Holocene. Radiocarbon dating of bulk sediment samples showed the presence of old carbon in the system, creating an age offset between 1,300 ± 200 and 2,800 ± 200 calibrated 14C years compared to the age-depth curve based on the terrestrial macrofossils. This finding, along with the strong marine influence in the system, discerned through geochemical data, dinoflagellate cyst and mollusc counts, is important for obtaining accurate radiocarbon ages in the region and stresses the importance of understanding both the marine and freshwater reservoir effects. The marine dominance in the eastern Limfjord differs from the west, which is characterized by a number of freshwater events when the North Sea connection was closed off during the Holocene. The eastern connection was open to the Kattegat throughout a large portion of the Holocene, with influx of open ocean water entering the system during periods of higher sea level.

Ultrastructure and phylogeny of peridinioid dinoflagellates

Os dinoflagelados são um grupo muito diverso de protistas que possuem um conjunto de características pouco comuns. Os peridinióides são dinoflagelados com teca que é formada por seis séries latitudinais de placas, incluindo a série cingular e um anel incompleto de placas intercalares anteriores, embora as últimas estejam ausentes em algumas espécies de Peridiniopsis. São dinoflagelados com simetria bilateral em relação ao plano apical que contem o eixo dorso-ventral. Na série sulcal há apenas uma placa posterior que contacta com o limite ventral de duas grandes placas antapicais. Entre os peridinióides, a presença ou ausência de um poro apical e o número de placas no cíngulo são geralmente consideradas marcas filogenéticas importantes ao nível de género ou família. Actualmente, a definição de Peridinium Ehrenberg, o dinoflagelado mais comum de água doce, inclui organismos com combinações diferentes destas duas características. Trabalhos anteriores sobre a ultrastrutura e afinidade filogenética das espécies tipo de Peridinium, P. cinctum, e Peridiniopsis Lemmermann, P. borgei também sugerem a necessidade de reexaminar as relações taxonómicas dos peridinióides. Esta tese combina o estudo ultrastrutural de uma selecção de espécies com hipóteses filogenéticas baseadas nas sequências de LSU rDNA, para aumentar o nosso conhecimento das diferenças e afinidades dentro dos peridinióides. Tem como objectivo aumentar o nosso conhecimento das características individuais das células que possam levar a reconhecer sinapomorfias que possam ser usadas como marcadores dos peridinióides como um todo e dos seus subgrupos. As espécies escolhidas para exame pormenorizado foram: Peridinium palatinum Lauterborn, de um grupo com duas placas intercalares anteriores, seis placas cingulares e sem poro apical; Peridinium lomnickii Wo!oszy"ska, de um grupo com poro apical, três placas intercalares e seis cingulares; Peridiniopsis berolinensis (Lemmermann) Bourrelly, uma espécie heterotrófica com poro apical, sem placas intercalares e com seis placas cingulares; e Sphaerodinium cracoviense Wo!oszy"ska, um membro de um género de formas com teca com um tipo de tabulação marginalmente peridinióide, com um suposto poro apical e quatro placas intercalares anteriores. Peridinium palatinum difere de Peridinium e Peridiniopsis típicos, quer em características da teca, quer internas. As diferenças estimadas entre as sequências parciais de LSU rDNA de P. palatinum e a espécie próxima P. pseudolaeve, relativamente a P. cinctum são comparativamente grandes e, juntamente com a topologia da árvore filogenética, apoiam a separação de P. palatinum e formas próximas ao nível de género. Palatinus nov. gen. foi, então, descrito com as novas combinações Palatinus apiculatus nov. comb. (espécie tipo; sin. Peridinium palatinum), P. apiculatus var. laevis nov. comb. e P. pseudolaevis nov. comb.. As características distintivas de Palatinus incluem uma superfície das placas lisa ou um tanto granulosa, mas não areolada, um grande pirenóide central penetrado por canais citoplasmáticos e de onde radiam lobos plastidiais, e a presença de uma fiada microtubular homóloga à de um pedúnculo. As células de Palatinus saem da teca pela zona antapicalpos- cingular. Peridinium lomnickii apresenta tabulação semelhante às formas marinhas, produtoras de quistos calcários, do género Scrippsiella A.R. Loeblich. Para comparação, adicionámos novas observações ultrastruturais de S. trochoidea. Peridinium lomnickii tem uma combinação de características diferente de Peridinium, Peridiniopsis e Scrippsiella. As hipóteses filogenéticas baseadas em DNA colocam P. lomnickii no mesmo ramo que Pfiesteria Steidinger et Burkholder, Tyrannodinium e outras Pfiesteriaceae, com as quais partilha um "microtubular basket" e uma ligação peculiar entre duas placas do sulco. As características distintivas do novo género proposto Chimonodinium gen. ined. incluem, além da tabulação, a ausência de pirenóides, a presença de um "microtubular basket" com quatro ou cinco fiadas sobrepostas de microtúbulos associados a um pequeno pedúnculo, um sistema pusular com tubos pusulares bem definidos ligados aos canais flagelares, e a produção de quistos não calcários. Peridiniopsis berolinensis partilha várias características significativas com Pfiesteria e afins, como um "microtubular basket" com a capacidade de suportar um tubo de alimentação, quimiossensibilidade para encontrar presas apropriadas, o modo de natação junto às presas e a organização geral da célula. Hipóteses filogenéticas com base em LSU rDNA confirmam a afinidade entre P. berolinensis e Pfiesteria bem como a relação mais remota com a espécie tipo de Peridiniopsis, P. borgei. Estas razões justificam a proposta de Tyrannodinium gen. nov., uma nova Pfiesteriaceae que difere de outros membros do grupo por viver em água doce e nos pormenores da tabulação. Sphaerodinium cracoviense revelou a tabulação típica do género Sphaerodinium, que apresenta um número de placas intercalares superiores e pos-cingulares maior que o que é típico em peridinióides: 4 e 6, respectivamente. Observações em SEM mostraram uma estrutura apical diferente da dos peridinióides, e um sulco apical numa das placas fazendo lembrar a área apical de alguns woloszynskióides. Os pormenores do aparelho flagelar e do sistema pusular ligam o Sphaerodinium aos woloszynskióides em geral e ao género Baldinia em particular, mas não aos peridinióides. O volumoso estigma de S. cracoviense revelou ser extraplastidial e de um modelo único, composto por elementos que se encontram em woloszynskióides, mas nunca encontrados anteriormente juntos. A análise filogenética baseada nas sequências parciais de LSU rDNA também sugerem uma maior proximidade de S. cracoviense com os woloszynskióides do que com os peridinióides. Futuras análises pormenorizadas de dinoflagelados peridinióides, em especial entre os do numeroso grupo de espécies com poro apical, serão necessárias para clarificar as suas relações taxonómicas; e a produção de descrições melhoradas das características finas particulares das células serão um requisito para perceber a evolução dos caracteres dos peridinióides por forma a podermos identificar marcadores filogenéticos.

Organic-walled dinoflagellate cysts in recent sediments from the Guadiana river estuary, South-East Portugal

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2007

Recent changes to the biogeochemistry of Muchalat Inlet, B.C., and the implications for HABs

Senior thesis written for Oceanography 445

Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics

Driver mutations in the two histone 3.3 (H3.3) genes, H3F3A and H3F3B, were recently identified by whole genome sequencing in 95% of chondroblastoma (CB) and by targeted gene sequencing in 92% of giant cell tumour of bone (GCT). Given the high prevalence of these driver mutations, it may be possible to utilise these alterations as diagnostic adjuncts in clinical practice. Here, we explored the spectrum of H3.3 mutations in a wide range and large number of bone tumours (n 5 412) to determine if these alterations could be used to distinguish GCT from other osteoclast-rich tumours such as aneurysmal bone cyst, nonossifying fibroma, giant cell granuloma, and osteoclast-rich malignant bone tumours and others. In addition, we explored the driver landscape of GCT through whole genome, exome and targeted sequencing (14 gene panel). We found that H3.3 mutations, namely mutations of glycine 34 in H3F3A, occur in 96% of GCT. We did not find additional driver mutations in GCT, including mutations in IDH1, IDH2, USP6, TP53. The genomes of GCT exhibited few somatic mutations, akin to the picture seen in CB. Overall our observations suggest that the presence of H3F3A p.Gly34 mutations does not entirely exclude malignancy in osteoclast-rich tumours. However, H3F3A p.Gly34 mutations appear to be an almost essential feature of GCT that will aid pathological evaluation of bone tumours, especially when confronted with small needle core biopsies. In the absence of H3F3A p.Gly34 mutations, a diagnosis of GCT should be made with caution.

Molecular epidemiology of Aspergillus collected from cystic fibrosis patients

Background - Aspergillus respiratory infection is a common complication in cystic fibrosis (CF) and is associated with loss of pulmonary function and allergic disease. Methods - Fifty-three Aspergillus isolates recovered from CF patients were identified to species by Internal Transcribed Spacer Region (ITS), β-tubulin, and calmodulin sequencing. Results - Three species complexes (Terrei, Nigri, and Fumigati) were found. Identification to species level gave a single Aspergillus terreus sensu stricto, one Aspergillus niger sensu stricto and 51 Aspergillus fumigatus sensu stricto isolates. No cryptic species were found. Conclusions - To our knowledge, this is the first prospective study of Aspergillus species in CF using molecular methods. The paucity of non-A. fumigatus and of cryptic species of A. fumigatus suggests a special association of A. fumigatus sensu stricto with CF airways, indicating it likely displays unique characteristics making it suitable for chronic residence in that milieu. These findings could refine an epidemiologic and therapeutic approach geared to this pathogen.