Portal protein diversity and phage ecology

© 2008 The Authors. This article is distributed under the terms of the Creative Commons License, Attribution 2.5. The definitive version was published in Environmental Microbiology 10 (2008): 2810-2823, doi:10.1111/j.1462-2920.2008.01702.x.Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.This research was supported in part by funding from NSF (CMORE contribution #87), DOE, The Seaver Foundation and the Gordon and Betty Moore Foundation Marine Microbiology Program to S.W.C.; an NIH Bioinformatics Training Grant supported M.B.S.; MIT Undergraduate Research Opportunities Program supported V.Q., J.A.L., G.T., R.F. and J.E.R.; Howard Hughes Medical Institute funded MIT Biology Department Undergraduate Research Opportunities Program supported A.S.D.; NSERC (Canada) Discovery Grant (DG 298394) and a Grant from the Canadian Foundation for Innovation (NOF10394) to J.P.B.; NSF Graduate Fellowship funding supported M.L.C

Corrigendum "Portal protein diversity and phage ecology"

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 13 (2011): 2832, doi:10.1111/j.1462-2920.2011.02616.x

Some recent radio talks.

Light land development in the South - By A. S. WILD, Assistant Superintendent of Wheat Farming, Department of Agriculture. It is only since World War II ended that successful large scale development of light land near the south coast of this State has been undertaken, although the many millions of acres of treeless plain country throughout the agricultural areas have, for many years, presented a challenge to the pioneering ability of Western Australians. The use of hormones in viticulture - By L. T. JONES, Senior Plant Research Officer The discovery and proper use of plant hormones, or as they are more accurately termed, growth-regulating: substances, probably represents the greatest contribution which science has made to agriculture in the past few decades. It was the discovery by Kogl in 1934 that indole acetic acid was an active growth substance which led rapidly to the preparation and testing of large numbers of compounds of similar chemical structure and among these were found many substances which were very potent and also comparatively cheap to produce. Recent trends in viticulture in Western Australia - By W. R. JAMIESON, Viticulturist, Department of Agriculture, Perth Today I want to talk very briefly about some of the more recent trends in viticulture in this State. The commercial production of grapevines is centred mainly around the Swan Valley and as most of the suitable vineyard land in this area has been planted, growers are exploring avenues to increase the returns per acre. Methods of irrigation - By G. GAUNTLETT, Assistant Officer-in-Charge, Irrigation The success of an irrigation scheme depends on several factors. Important among these is the choice and design of the method to be adopted. There are two methods of irrigation, viz., surface and spray irrigation. Canker disease of Red-flowered gum - By W. P. CASS SMITH, B.Sc. (Agric), Government Plant Pathologist Of the many beautiful native plants in Western Australia, few are esteemed more than the red-flowered gum known botanically as Eucalyptus flcifolia. This shapely tree commences blossoming about Christmas time—and provides a magnificent display for several weeks—the blossom shades varying from dark red to pink. Why many beans grow crooked - By M. HARDIE, Vegetable Instructor Sometimes in the process of growing a crop, bean growers find a number of pods which, instead of being long and straight and suitable for marketing, are crooked or bent and quite unsuitable for sale unless beans are in very short supply. It is not unusual for a small number of pods to be affected in this way, generally at the tail-end of the crop, but occasionally the percentage may be high. When this happens the grower is often at a loss to account for his failure to grow a marketable crop. To the best of his ability he has followed methods which normally return a crop of first-grade pods and yet for some reason, his crop is an unpayable one and he is anxious to ascertain the cause. Salt land programme for Autumn - By T. C. STONEMAN, Adviser, Soil Conservation Service Now that summer is over and winter approaches, the time has come to decide what you\u27ll do with that salt problem on your farm. What you SHOULD do, will depend on how severely the area is affected. To make quite clear how the recommendations made by the Department of Agriculture can be applied I will deal with each degree of severity in turn. Orchard cover crops - By J. CRIPPS, Horticultural Adviser The sowing of a cover crop is one of those routine operations which the orchardist often undertakes without much thought, but it is an operation worthy of consideration. Lupin seed - By B. J. QUINLIVAN, B.Sc. (Agric), Botanist, Weeds and Seeds Branch The three types of lupins which we grow in this State are the New Zealand, the W.A. blue, and the yellow lupin. The first two types are very common, the New Zealand lupin being grown mainly in the South-West, while the W.A. lupin is grown over extensive areas of the central and northern wheatbelt, particularly on the sandier types of soil. Cereal rye will grow on wind-eroded areas - By G. H. BURVILL, Chief Plant Research Officer. Travelling around the wheatbelt, one often sees areas of sandy soil quite bare, A due to wind erosion. Surface soil blown from these patches has built up against fences, or as mounds in the nearby scrub. Many of the eroded places are quite small— perhaps less than an acre or only a few acres. But some are large, with one to three hundred acres of bare yellow sand. As much as two feet of soil has been blown from big areas. Autumn-winter feeding for the fat lamb flock - By N. DAVENPORT, Senior Adviser, Meat Production The autumn-winter period is the most important part of the year for the fat lamb crop from a feed point of view. It is important not only from the aspect of the wellbeing of the sheep, but also of the pasture. Pasture plants are living things, too, and they also require consideration and care for their development. When a new season pasture is kept hard grazed in those critical first few weeks of growth it cannot carry as many sheep over the season as one which is lightly stocked during that time. Plant diseases in the home garden - By W. P. CASS-SMITH, B.Sc. (Agric), Government Plant Pathologist Recently many home-gardeners have complained that plantings of vegetables or ornamentals are making unthrifty growth, in spite of liberal waterings and fertilisation. These symptoms are commonly caused by root-knot eelworm, a pest which has unfortunately become very widespread in the sandy soils adjacent to Perth, and in many other parts of this State. This eelworm parasite attacks the roots of many kinds of plants causing them to rot and to develop bead-like swellings or galls. As a result, the intake of plant food and water is restricted and stunting of the above-ground parts occurs. Principles of commercial beekeeping - By R. S. COLEMAN, R.D.A., Government Apiculturist We have many queries from small beekeepers, and from people who have never opened a hive, on how to break into full-time beekeeping. So it was thought that you would like to know just what are the principles of successful bee farming. Grasshoppers and locusts - By C. F. H. JENKINS, M.A., Government Entomologist Grasshoppers and locusts are among the most ancient enemies of mankind for they figured prominently in Biblical times, and periodically throughout the ages have devastated crops in all parts of the world. Acetonaemia in dairy cattle - By P. M. A. HARWOOD, M.R.C.V.S., Veterinary Officer Acetonaemia, more correctly known as ketosis is a metabolic disease. Unlike infectious diseases such as tuberculosis or mastitis, which are caused by microbes, metabolic diseases result from an upset in the normal bodily processes. Molybdenum for subterranean clover - By T. C. DUNNE, B.Sc. (Agric), Ph.D. (Calif.), Chief Plant Nutrition and Research Officer Subterranean clover is undoubtedly the most important pasture species in this State. Because it is a legume, it can make excellent growth on soils with a low nitrogen content. The nitrogen it needs is, of course, provided by bacteria which inhabit the nodules found on its roots. These bacteria provide nitrogen by taking it from the air and converting it to a form which can be used by the clover. However, it is now known that the bacteria can use the nitrogen of the air only if enough molybdenum is available to them. Cobalt deficiency in sheep and cattle - By C. R. TOOP, B.V.SC, Chief Veterinary Officer With the establishment of group settlements at Denmark after the first world war, it was observed that young cattle, although running on lush pastures, developed systems of unthriftness and wasting and usually died. Research conducted of Filmer and Underwood later revealed that this condition was caused by a deficiency of cobalt and that it could be cured and prevented by addition of this mineral to the diet. Cobalt deficiency has since been met with other parts of the State and was recently diagnosed in sheep at Mount Manypeaks

Influence of operating parameters on the biodegradation of steroid estrogens and nonylphenolic compounds during biological wastewater treatment processes

This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Environmental Science & Technology, copyright © American Chemical Society after peer review. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/es901612v.This study investigated operational factors influencing the removal of steroid estrogens and nonylphenolic compounds in two sewage treatment works, one a nitrifying/denitrifying activated sludge plant and the other a nitrifying/denitrifying activated sludge plant with phosphorus removal. Removal efficiencies of >90% for steroid estrogens and for longer chain nonylphenol ethoxylates (NP4−12EO) were observed at both works, which had equal sludge ages of 13 days. However, the biological activity in terms of milligrams of estrogen removed per day per tonne of biomass was found to be 50−60% more efficient in the nitrifying/denitrifying activated sludge works compared to the works which additionally incorporated phosphorus removal. A temperature reduction of 6 °C had no impact on the removal of free estrogens, but removal of the conjugated estrone-3-sulfate was reduced by 20%. The apparent biomass sorption (LogKp) values were greater in the nitrifying/denitrifying works than those in the nitrifying/denitrifying works with phosphorus removal for both steroid estrogens and nonylphenolic compounds possibly indicating a different cell surface structure and therefore microbial population. The difference in biological activity (mg tonne−1 d−1) identified in this study, of up to seven times, suggests that there is the potential for enhancing the removal of estrogens and nonylphenols if more detailed knowledge of the factors responsible for these differences can be identified and maximized, thus potentially improving the quality of receiving waters.Public Utilities Board (Singapore), Anglian Water Ltd, Severn Trent Water Ltd, Thames Water Utilities Ltd, United Utilities 393 Plc and Yorkshire Water Services

The effect of antidepressant treatment on HIV and depression outcomes: results from a randomized trial

Depression is a major barrier to HIV treatment outcomes

CAV3 mutations causing exercise intolerance, myalgia and rhabdomyolysis: expanding the phenotypic spectrum of caveolinopathies

Rhabdomyolysis is often due to a combination of environmental trigger(s) and genetic predisposition; however, the underlying genetic cause remains elusive in many cases. Mutations in CAV3 lead to various neuromuscular phenotypes with partial overlap, including limb girdle muscular dystrophy type 1C (LGMD1C), rippling muscle disease, distal myopathy and isolated hyperCKemia. Here we present a series of eight patients from seven families presenting with exercise intolerance and rhabdomyolysis caused by mutations in CAV3 diagnosed by next generation sequencing (NGS) (n=6). Symptoms included myalgia (n=7), exercise intolerance (n=6) and episodes of rhabdomyolysis (n=2). Percussion-induced rapid muscle contractions (PIRCs) were seen in five out of six patients examined. A previously reported heterozygous mutation in CAV3 (p.T78M) and three novel variants (p.V14I, p.F41S, p.F54V) were identified. Caveolin-3 immunolabeling in muscle was normal in 3/4 patients however, immunoblotting showed more than 50% reduction of caveolin-3 in five patients compared with controls. This case series demonstrates that exercise intolerance, myalgia and rhabdomyolysis may be caused by CAV3 mutations and broadens the phenotypic spectrum of caveolinopathies. In our series immunoblotting was a more sensitive method to detect reduced caveolin-3 levels than immunohistochemistry in skeletal muscle. Patients presenting with muscle pain, exercise intolerance and rhabdomyolysis should be routinely tested for PIRCs as this may be an important clinical clue for caveolinopathies, even in the absence of other “typical” features. The use of NGS may expand current knowledge concerning inherited diseases, and unexpected/atypical phenotypes may be attributed to well-known human disease genes

Malignant hyperthermia

Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle that presents as a hypermetabolic response to potent volatile anesthetic gases such as halothane, sevoflurane, desflurane and the depolarizing muscle relaxant succinylcholine, and rarely, in humans, to stresses such as vigorous exercise and heat. The incidence of MH reactions ranges from 1:5,000 to 1:50,000–100,000 anesthesias. However, the prevalence of the genetic abnormalities may be as great as one in 3,000 individuals. MH affects humans, certain pig breeds, dogs, horses, and probably other animals. The classic signs of MH include hyperthermia to marked degree, tachycardia, tachypnea, increased carbon dioxide production, increased oxygen consumption, acidosis, muscle rigidity, and rhabdomyolysis, all related to a hypermetabolic response. The syndrome is likely to be fatal if untreated. Early recognition of the signs of MH, specifically elevation of end-expired carbon dioxide, provides the clinical diagnostic clues. In humans the syndrome is inherited in autosomal dominant pattern, while in pigs in autosomal recessive. The pathophysiologic changes of MH are due to uncontrolled rise of myoplasmic calcium, which activates biochemical processes related to muscle activation. Due to ATP depletion, the muscle membrane integrity is compromised leading to hyperkalemia and rhabdomyolysis. In most cases, the syndrome is caused by a defect in the ryanodine receptor. Over 90 mutations have been identified in the RYR-1 gene located on chromosome 19q13.1, and at least 25 are causal for MH. Diagnostic testing relies on assessing the in vitro contracture response of biopsied muscle to halothane, caffeine, and other drugs. Elucidation of the genetic changes has led to the introduction, on a limited basis so far, of genetic testing for susceptibility to MH. As the sensitivity of genetic testing increases, molecular genetics will be used for identifying those at risk with greater frequency. Dantrolene sodium is a specific antagonist of the pathophysiologic changes of MH and should be available wherever general anesthesia is administered. Thanks to the dramatic progress in understanding the clinical manifestation and pathophysiology of the syndrome, the mortality from MH has dropped from over 80% thirty years ago to less than 5%

Ovine Fetal Thymus Response to Lipopolysaccharide-Induced Chorioamnionitis and Antenatal Corticosteroids

RATIONALE: Chorioamnionitis is associated with preterm delivery and involution of the fetal thymus. Women at risk of preterm delivery receive antenatal corticosteroids which accelerate fetal lung maturation and improve neonatal outcome. However, the effects of antenatal corticosteroids on the fetal thymus in the settings of chorioamnionitis are largely unknown. We hypothesized that intra-amniotic exposure to lipopolysaccharide (LPS) causes involution of the fetal thymus resulting in persistent effects on thymic structure and cell populations. We also hypothesized that antenatal corticosteroids may modulate the effects of LPS on thymic development. METHODS: Time-mated ewes with singleton fetuses received an intra-amniotic injection of LPS 7 or 14 days before preterm delivery at 120 days gestational age (term = 150 days). LPS and corticosteroid treatment groups received intra-amniotic LPS either preceding or following maternal intra-muscular betamethasone. Gestation matched controls received intra-amniotic and maternal intra-muscular saline. The fetal intra-thoracic thymus was evaluated. RESULTS: Intra-amniotic LPS decreased the cortico-medullary (C/M) ratio of the thymus and increased Toll-like receptor (TLR) 4 mRNA and CD3 expression indicating involution and activation of the fetal thymus. Increased TLR4 and CD3 expression persisted for 14 days but Foxp3 expression decreased suggesting a change in regulatory T-cells. Sonic hedgehog and bone morphogenetic protein 4 mRNA, which are negative regulators of T-cell development, decreased in response to intra-amniotic LPS. Betamethasone treatment before LPS exposure attenuated some of the LPS-induced thymic responses but increased cleaved caspase-3 expression and decreased the C/M ratio. Betamethasone treatment after LPS exposure did not prevent the LPS-induced thymic changes. CONCLUSION: Intra-amniotic exposure to LPS activated the fetal thymus which was accompanied by structural changes. Treatment with antenatal corticosteroids before LPS partially attenuated the LPS-induced effects but increased apoptosis in the fetal thymus. Corticosteroid administration after the inflammatory stimulus did not inhibit the LPS effects on the fetal thymus

Insights into pathogenic events of HIV-associated Kaposi sarcoma and immune reconstitution syndrome related Kaposi sarcoma

A decrease in the incidence of human immune deficiency virus-associated Kaposi sarcoma (HIV-KS) and regression of some established HIV-KS lesions is evident after the introduction of highly active anti-retroviral treatment (HAART), and is attributed to generalized immune restoration, to the reconstitution of human herpesvirus (HHV)-8 specific cellular immune responses, and to the decrease in HIV Tat protein and HHV-8 loads following HAART. However, a small subset of HIV-seropositive subjects with a low CD4+ T cell count at the time of introduction of HAART, may develop HIV-KS as immune reconstitution inflammatory syndrome (IRIS) within 8 weeks thereafter

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

BACKGROUND: The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection. METHODS: We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis. RESULTS: Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives. CONCLUSIONS: Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.)