Grassland intensification dramatically impacts grasshoppers: Experimental evidence for direct and indirect effects of fertilisation and irrigation

European mountain hay meadows are hosting an exceptionally rich biodiversity. They are currently threatened by both land abandonment and farming intensification via aerial irrigation and slurry application. The consequences of mountain grassland intensification on arthropods are still poorly documented, which is a serious handicap to proposing ecologically-friendly management guidance. Six experimental treatments mimicking a gradient of management intensity (including irrigation, fertilisation and various combinations thereof) were initiated in 2010 at twelve montane and subalpine Swiss meadow sites. In 2013, we sampled orthopterans to assess the influence of management practice on that taxonomic group. In parallel, the changes in vegetation height and ambient temperature (at 10 cm above ground level) induced by the intensification process were quantified in order to better appraise the underlying mechanisms. Intensification had a negative impact on Caelifera (grasshoppers), with decreases in densities and species richness reaching as much as 70% and 50%, respectively, in the most intensively managed treatment plots. Intensification furthermore led to a marked increase in mean vegetation height and a cooling of ambient temperature by up to 4.2 ◦C. Such microhabitat and microclimate alterations are likely to affect Caelifera development, in particular thermophilous species. In contrast, Ensifera (bushcrickets) densities and species richness showed no significant response to our experimental manipulations. Finally, the application of irrigation by sprinklers alone had limited impact on both orthopterans and meadow microclimate. We conclude that orthopterans, in particular Caelifera, are fairly sensitive to grassland management intensification: fertilisation should be avoided in focal areas for biodiversity conservation

Exile Vol. LII No. 2

Title Page 2 Epigraph by Ezra Pound 3 Table of Contents 4 Editor\u27s Note 6 Contributors\u27 Notes 45 Editorial Board 46 ART Wallace Monument by Casey Flax 9 Blind Man by Abbe Wright 18 Untitled by Adrienne Hunter 20 Sentinel by Eric Ahnmark 28 Untitled by Abbe Wright 32 Under Charles by Medha Jaishankar 43 FICTION The Great Lego Wall by Dawson West 12-16 Gods by Nick Wright 21-24 Some Days Hit like Mack Trucks by Sarah Broderick 33-42 POETRY The Liberation from Jack Kerouac by Katie Berta 7-8 Fragmented Grief by Jen Humbert 10 Rauschenberg Painting Iris Clért by Jeremy Heartberg 11 Outgrowing by Sarah Rogers 17 Garden of Eden by Jen Humbert 19 She whispered to the moon by Dave Murrin-von Ebers 25 A Joke by Jeremy Heartberg 26 Retrospective by Casey Flax 27 Ketchup Fetish by Dawson West 29 Winter Raspberries by Jennifer Luebbers 30-31 Knot by Sarah Rogers 44 Editor\u27s Note The process by which Exile comes into being each semester is by no means a quick or simple one, and was further confounded in this instance by having me at its core. I do not necessarily mean to discredit myself ad nauseam as some editors would, but they will all tell you that transitional periods are the toughest on a publication. The collaborative effort of Jeremy Heartberg and Jennifer Humbert over the past several semesters, not to mention the competent and eager editorial staff they have recruited, has seen to it that the transition made in these past few months has not been bulky or awkward, but rather quite seamless. It is appropriate then, that the two of them are both prominently featured in the edition of Exile on which you presently fix your gaze. In recent years, you have benefited from Jeremy\u27s and Jen\u27s dedication to Exile as a whole; this year, enjoy their dedication to the flexibility and nuance of language, to the manipulation of form, to poetry. Jeremy, Jen, Sarah, and Emily, thank you, you will be missed. / April 2006 -6 Front Cover Art by Chris Davis: Reflections / Back Cover Art by Eric Ahnmark: Trucks Only -46 All submissions are reviewed on an anonymous basis, and all editorial decisions are shared equally among the members of the editorial board. -4

Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads

Inselberg-adapted species of bromeliads (Bromeliaceae) have been suggested as model systems for understanding the evolutionary genetics of species complexes and radiations in terrestrial, island-like environments. Bromeliads are particularly suitable for addressing the potential roles of interspecific gene exchange during plant speciation and radiation. We have studied populations of five narrowly endemic Alcantarea species adapted to high-elevation inselbergs of the Atlantic Rainforest of Brazil with nuclear and plastid DNA markers, estimated outcrossing rates in the giant bromeliad A. imperialis using progeny arrays and carried out a pilot study on the use of next generation sequencing-based genotyping in this group. Our results suggest widespread and asymmetric interspecific gene flow in the studied species complex, which visibly affects patterns of genetic diversity in the phenotypically variable mixed outcrosser A. imperialis. Our data support the hypothesis that gene flow has contributed to the origin of phenotypic forms in the A. imperialis s.l. species complex. We discuss potential conflicts between our neutral marker data and previous taxonomic work and suggest how these might be resolved. We close with a brief outlook on the potential of genomic tools to uncover the hidden links between genotypes, phenotypes and niches in bromeliads and other plant radiations

Collage Vol. II

JUDY COCHRAN: Editorial, 4-5 ROBERTA CHAPMEN: Photo, 6 ANITRA CHUGHTAI (Translations): Haikus, 7 CHARLES O\u27KEEFE: Photo, 8 MARK VANDERLINDE-ABERNATHY, ALYSSA LANDRY (Translator): Memories of a Spider (Les souvenirs d\u27une araignee), 9 MARK VANDERLINE-ABERNATHY, AMY NORSKOG (Translator): Tomato Fields (Champ de tomates), 10 SARAH BISHOP, HEFEDH ZANINA (Translator): Dear John (Cher John), 11 RYAN BUTZ (Translator): Basho\u27s Haiku, Issa\u27s Haiku, 12-13 JENNIFER HUMBERT, FADOUA EL BOUAMRAOUI (Translator): Pressed Lips (Levres Serrees), 15 ADELE REEVES (Translator): Contemporary song by Mr. Children, 16-17 BRODY PAGEL, GRACE DUGAR (Translator): The Lizard King (Le Roi Lezard), 18 JIMMY PIPKIN (Translator): In Love with You, 19 MOLLY ROSCOE: Saturday Night at Rusty\u27s (Samedi Soir a Rusty\u27s), 20 CHARLES O\u27KEEFE: Photo, 21 MATT MESSMER (Translator): Waseda University School Song, 22-23 TIMOTHY COOPER: Wenn du grosh bist… (When you\u27re Tall…), 24 DAVID HARMAN: Der Dunkle Stern (The Dark Star), 25 ANN TOWNSEND, JUDY COCHRAN (Translator): From a Window (D\u27une Fenetre), 26-27 SARA CAHILL: El sauce lloron (The Weeping Willow), 28-32 CHARLES O\u27KEEFE: Photo, 30 JENNIFER HUMBERT, MATT BISHOP: Past, Present (passe, present), 33 CAROL GENEYA KAPLAN, FADOUA EL BOUAMRAOUI (Translator): Une Autre Femme (Another Woman), 34-35 CHARLES O\u27KEEFE: Photo, 36 ANN TOWNSEND, JUDY COCHRAN (Translator): The Mowers (Les Faucheurs), 37 PRISCILLA PATON: Photo, 38 GONZALO TUESTA: La Grande Dame De Paris (The Great Lady of Paris), 39 SARAH PILLERDORF (Translator): Japanese Cartoons by Tezuka Osamu, 41-45 DANIELLE GERKEN: Schuhe der Heimat (Boots of Home), 47 CURTIS PLOWGIAN: Le peste de la langue francaise, 48-52 PRISCILLA PATON: Photo, 50 ZANE HOUSEHOLDER: Vive la Republique! (Film), 54 JENNIFER ZIMMER: EL tenis y las frustraciones (Tennis and Frustrations), La tumba de Ben (Ben\u27s Grave), 56-57 AUTUMN LOTZE: Times Square in the rain, 58-59 CHARLES O\u27KEEFE: Photo, 60 STEPHEN M. JULKA: Colors of the Earth, 61 THOMAS BRESSOUD: Java, 62 ERIC NELSON: World, 63 SARAH CLAPP (Translator): At a long day\u27s end (Natsume Soseki), A friend has come and is now leaving, Eating persimmons (Masaoka Shiki), 64 CHARLES O\u27KEEFE: Photo, 65 JOHN BURZYNSKI, MEGAN FETTER (Translator): Home is where the heart is, 66 RICHARD BANAHAN: Photo, 67 KIM FREEMAN: Baltimore, 68 JACOB RIDRIGUEZ-NOBLE: Home (Heimat), 69 SUZANNE KENNEDY: Oft verberge ich mich (Oft I hide myself), 70 RICHARD BANAHAN: Photo, 7

From bones to blood pressure, developing novel biologic approaches targeting the osteoprotegein pathway for pulmonary vascular disease.

Osteoprotegerin (tnfsf11b, OPG) is a soluble member of the TNF superfamily originally described as an important regulator of osteoclastogenesis almost 20years ago. OPG is a heparin-binding secreted glycoprotein that exists as a 55-62kDa monomer or a 110-120kDa disulphide-linked homodimer. Acting as a soluble decoy receptor for RANKL, OPG actively regulates RANK signalling, and thereby osteoclastogenesis. OPG has subsequently been shown to also be a decoy receptor TNF related apoptosis inducing-ligand (tnfsf10, TRAIL, Apo2L). TRAIL is a type II transmembrane protein that is widely expressed in a variety of human tissues, including the spleen, lung, and prostate. Through binding to TRAIL, OPG can inhibit TRAIL-induced apoptosis of cancer cells. More recently OPG has been demonstrated to be secreted by, and influence, vascular smooth muscle cells phenotype particularly related to vascular calcification and pulmonary vascular remodelling. In pulmonary artery smooth muscle cell (PASMC) suppression of BMP, and induction of 5-HT and IL-1 signalling have been shown to stimulate the release of OPG in vitro, which causes cell migration and proliferation. Patients with idiopathic PAH (IPAH) demonstrate increased circulating and tissue levels of OPG, and circulating serum levels predict survival. In pre-clinical models OPG levels correlate with disease severity. Since OPG is a naturally circulating protein we are investigating the potential of novel biologic antibody therapies to rescue PAH phenotype in disease models. Further pre-clinical and mechanistic data are forthcoming but we believe current published data identifies OPG as an exciting and novel therapeutic target in PAH

Helicobacter pylori's Unconventional Role in Health and Disease

The discovery of a bacterium, Helicobacter pylori, that is resident in the human stomach and causes chronic disease (peptic ulcer and gastric cancer) was radical on many levels. Whereas the mouth and the colon were both known to host a large number of microorganisms, collectively referred to as the microbiome, the stomach was thought to be a virtual Sahara desert for microbes because of its high acidity. We now know that H. pylori is one of many species of bacteria that live in the stomach, although H. pylori seems to dominate this community. H. pylori does not behave as a classical bacterial pathogen: disease is not solely mediated by production of toxins, although certain H. pylori genes, including those that encode exotoxins, increase the risk of disease development. Instead, disease seems to result from a complex interaction between the bacterium, the host, and the environment. Furthermore, H. pylori was the first bacterium observed to behave as a carcinogen. The innate and adaptive immune defenses of the host, combined with factors in the environment of the stomach, apparently drive a continuously high rate of genomic variation in H. pylori. Studies of this genetic diversity in strains isolated from various locations across the globe show that H. pylori has coevolved with humans throughout our history. This long association has given rise not only to disease, but also to possible protective effects, particularly with respect to diseases of the esophagus. Given this complex relationship with human health, eradication of H. pylori in nonsymptomatic individuals may not be the best course of action. The story of H. pylori teaches us to look more deeply at our resident microbiome and the complexity of its interactions, both in this complex population and within our own tissues, to gain a better understanding of health and disease

Identification of Pik3ca mutation as a genetic driver of prostate cancer that cooperates with Pten loss to accelerate progression and castration-resistant growth

Genetic alterations that potentiate PI3K signalling are frequent in prostate cancer, yet how different genetic drivers of the PI3K cascade contribute to prostate cancer is unclear. Here, we report PIK3CA mutation/amplification correlates with poor prostate cancer patient survival. To interrogate the requirement of different PI3K genetic drivers in prostate cancer, we employed a genetic approach to mutate Pik3ca in mouse prostate epithelium. We show Pik3caH1047R mutation causes p110-dependent invasive prostate carcinoma in-vivo. Furthermore, we report PIK3CA mutation and PTEN loss co-exist in prostate cancer patients, and can cooperate in-vivo to accelerate disease progression via AKT-mTORC1/2 hyperactivation. Contrasting single mutants that slowly acquire castration-resistant prostate cancer (CRPC), concomitant Pik3ca mutation and Pten loss caused de-novo CRPC. Thus, Pik3ca mutation and Pten deletion are not functionally redundant. Our findings indicate that PIK3CA mutation is an attractive prognostic indicator for prostate cancer that may cooperate with PTEN loss to facilitate CRPC in patients

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.This work was supported by The National Institute for Health Research England (NIHR) for the NIHR BioResource – Rare Diseases project (grant number RG65966). The Moorfields Eye Hospital cohort of patients and clinical and imaging data were ascertained and collected with the support of grants from the National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, National Health Service Foundation Trust, and UCL Institute of Ophthalmology, Moorfields Eye Hospital Special Trustees, Moorfields Eye Charity, the Foundation Fighting Blindness (USA), and Retinitis Pigmentosa Fighting Blindness. M.M. is a recipient of an FFB Career Development Award. E.M. is supported by UCLH/UCL NIHR Biomedical Research Centre. F.L.R. and D.G. are supported by Cambridge NIHR Biomedical Research Centre