Enrichment and characterization of ammonia-oxidizing archaea from the open ocean : phylogeny, physiology and stable isotope fractionation

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1796–1808, doi:10.1038/ismej.2011.58.Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the north Pacific Ocean that have been maintained in laboratory culture for over three years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S rRNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and cDNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonium (NH4 +) to nitrite (NO2 -). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13- 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.This work was supported by a Woods Hole Oceanographic Institution (WHOI) Postdoctoral Scholar fellowship to AES and the WHOI Ocean Life Institute

Pompe disease diagnosis and management guideline

ACMG standards and guidelines are designed primarily as an educational resource for physicians and other health care providers to help them provide quality medical genetic services. Adherence to these standards and guidelines does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. in determining the propriety of any specific procedure or test, the geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the patient's record the rationale for any significant deviation from these standards and guidelines.Duke Univ, Med Ctr, Durham, NC 27706 USAOregon Hlth Sci Univ, Portland, OR 97201 USANYU, Sch Med, New York, NY USAUniv Florida, Coll Med, Powell Gene Therapy Ctr, Gainesville, FL 32611 USAIndiana Univ, Bloomington, in 47405 USAUniv Miami, Miller Sch Med, Coral Gables, FL 33124 USAHarvard Univ, Childrens Hosp, Sch Med, Cambridge, MA 02138 USAUniversidade Federal de São Paulo, São Paulo, BrazilColumbia Univ, New York, NY 10027 USANYU, Bellevue Hosp, Sch Med, New York, NY USAColumbia Univ, Med Ctr, New York, NY 10027 USAUniversidade Federal de São Paulo, São Paulo, BrazilWeb of Scienc

Congenital Diaphragmatic hernia – a review

Congenital Diaphragmatic hernia (CDH) is a condition characterized by a defect in the diaphragm leading to protrusion of abdominal contents into the thoracic cavity interfering with normal development of the lungs. The defect may range from a small aperture in the posterior muscle rim to complete absence of diaphragm. The pathophysiology of CDH is a combination of lung hypoplasia and immaturity associated with persistent pulmonary hypertension of newborn (PPHN) and cardiac dysfunction. Prenatal assessment of lung to head ratio (LHR) and position of the liver by ultrasound are used to diagnose and predict outcomes. Delivery of infants with CDH is recommended close to term gestation. Immediate management at birth includes bowel decompression, avoidance of mask ventilation and endotracheal tube placement if required. The main focus of management includes gentle ventilation, hemodynamic monitoring and treatment of pulmonary hypertension followed by surgery. Although inhaled nitric oxide is not approved by FDA for the treatment of PPHN induced by CDH, it is commonly used. Extracorporeal membrane oxygenation (ECMO) is typically considered after failure of conventional medical management for infants ≥ 34 weeks’ gestation or with weight >2 kg with CDH and no associated major lethal anomalies. Multiple factors such as prematurity, associated abnormalities, severity of PPHN, type of repair and need for ECMO can affect the survival of an infant with CDH. With advances in the management of CDH, the overall survival has improved and has been reported to be 70-90% in non-ECMO infants and up to 50% in infants who undergo ECMO

Poleward decrease in the isotope effect of nitrate assimilation across the Southern Ocean

Recent studies provide seasonally and spatially resolved information on the isotopic characteristics of nitrate supply and N cycling in Southern Ocean surface waters. The new data improve our understanding of the nitrate supply to the Antarctic surface and its isotopic characteristics, especially with regard to the summertime subsurface minimum temperature (Tmin) layer in the Antarctic. We use these findings to update and compile estimates of the N isotope effect of nitrate assimilation, ε, in the Southern Ocean near Australia. A poleward decrease in ε emerges, from 8-9‰ in the Subantarctic Zone (SAZ, 40-52°S) to similar to 5‰ in the Polar Antarctic Zone (PAZ, ~66°S). ε is strongly correlated with mixed layer depth at the time of sampling. We hypothesize that the correlation is driven by the physiological response of diatoms to light availability, with light limitation leading to higher cellular efflux of nitrate and thus higher ε

Nitrogen isotope constraints on subantarctic biogeochemistry

We report nitrate (NO3 -) nitrogen isotope ratios for seawater samples collected in the Subantarctic Zone of the Southern Ocean during both winter and summer as part of the Australian Antarctic CRC Subantarctic Zone (SAZ) Project. The concentration and 15N/14N of the wintertime surface nitrate are very close to those of the subantarctic thermocline. The 15N/14N of nitrate in the surface increases sharply into the summer even though there is little seasonal change in nitrate concentration. There are two possible end-member explanations for this observation. First, there may be significant equatorward nitrate transport during the summer, including a supply from the Antarctic surface. Second, the isotope effect of algal nitrate assimilation may be higher than has been estimated elsewhere, for example, for the seasonal sea ice zone of the Antarctic. We use a simple geochemical box model of the SAZ surface mixed layer as it evolves over the course of the summer to simulate salinity, nitrate concentration, and the 15N/14N of nitrate and sinking N. Our results suggest that a significant portion (∼30%) of the summertime SAZ nitrate is supplied from south of the Subantarctic Front and that N export is ≥3.5 mmol N m-2 d-1. Our approach also identifies the necessity of an isotope effect for nitrate assimilation in the SAZ of ≥7‰ and probably 8-9‰. Comparison to laboratory results suggests that this relatively high isotope effect may result from light limitation of algal growth in the SAZ. Copyright 2006 by the American Geophysical Union

The influence of iron and light on net community production in the Subantarctic and Polar Frontal Zones

The roles of iron and light in controlling biomass and primary productivity are clearly established in the Southern Ocean. However, their influence on net community production (NCP) and carbon export remains to be quantified. To improve our understanding of NCP and carbon export production in the Subantarctic Zone (SAZ) and the northern reaches of the Polar Frontal Zone (PFZ), we conducted continuous onboard determinations of NCP as part of the Sub-Antarctic Sensitivity to Environmental Change (SAZ-Sense) study, which occurred in January-February 2007. Biological O2 supersaturation was derived from measuring O2/Ar ratios by equilibrator inlet mass spectrometry. Based on these continuous measurements, NCP during the austral summer 2007 in the Australian SAZ was approximately 43 mmol O2 m-2 d-1. NCP showed significant spatial variability, with larger values near the Subtropical front, and a general southward decrease. For shallower mixed layers (<50 m), dissolved Fe concentrations and Fe sufficiency, estimated from variable fluorescence, correlated strongly with NCP. The strong correlation between NCP and dissolved Fe may be difficult to interpret because of the correlation of dissolved Fe to MLD and because the concentration of iron may not be a good indicator of its availability. At stations with deeper mixed layers, NCP was consistently low, regardless of iron sufficiency, consistent with light availability also being an important control of NCP. Our new observations provide independent evidence for the critical roles of iron and light in mediating carbon export from the Southern Ocean mixed layer