A Single-Institution Review of Portosystemic Shunts in Children: An Ongoing Discussion

Purpose. Review the safety and long-term success with portosystemic shunts in children at a single institution. Methods. An IRB-approved, retrospective chart review of all children ages 19 and undergoing surgical portosystemic shunt from January 1990–September 2008. Results. Ten patients were identified, 8 females and 2 males, with a mean age of 15 years (range 5–19 years). Primary diagnoses were congenital hepatic fibrosis (5), hepatic vein thrombosis (2), portal vein thrombosis (2), and cystic fibrosis (1). Primary indications were repeated variceal bleeding (6), symptomatic hypersplenism (2), and significant liver dysfunction (2). Procedures performed were distal splenorenal bypass (4), side-to-side portocaval shunt (3), proximal splenorenal shunt (2), and an interposition H-graft portocaval shunt (1). There was no perioperative mortality and only minor morbidity. Seventy percent of patients had improvement of their symptoms. Eighty percent of shunts remained patent. Two were occluded at a median follow-up of 50 months (range 0.5–13.16 years). Two patients underwent subsequent liver transplantation. Two patients died at 0.5 and 12.8 years postoperatively, one from multisystem failure with cystic fibrosis and one from post-operative transplant complications. Conclusions. The need for portosystemic shunts in children is rare. However, in the era of liver transplantation, portosystemic shunts in selected patients with well-preserved liver function remains important. We conclude that portosystemic shunts are safe and efficacious in the control of variceal hemorrhage and symptoms related to hypersplenism

Changes in carabid beetle assemblages across an urban-rural gradient in Japan

As part of the international Globenet project, carabid beetles (Coleoptera, Carabidae) were collected using pitfall traps from four urban, four suburban and four rural sites in Hiroshima City, Japan, during the 2001 summer season. In agreement with expectation, carabid abundance and species richness decreased significantly from rural to urban sites. Furthermore, no large, and only few individuals of medium-sized specialist species were collected from the urban environment, while many specimens of medium-sized and some large-sized specialist species were collected from the suburban and rural sites. Hiroshima city was characterised by medium-sized generalist carabids, while the suburbs and the rural environments were characterised by small-sized generalist beetles. These results did not apply at the species level. To summarise, we found a significant effect of urbanisation on the composition of carabid beetle assemblages in Hiroshima City. These changes were similar to those found in previous studies performed in Sofia (Bulgaria), Edmonton (Canada) and Helsinki (Finland). Thus, it appears that urbanisation has some similar and predictable effects on carabid assemblages in various parts of the world

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.National Institutes of Health (U.S.) (Grant 5DP1-MH100706

Developing Methods to Evaluate Phenotypic Variability in Biological Nitrification Inhibition (BNI) Capacity of \u3cem\u3eBrachiaria\u3c/em\u3e Grasses

As part of the nitrogen (N) cycle in the soil, nitrification is an oxidation process mediated by microorganisms that transform the relatively immobile ammonium (NH4+)to the water soluble nitrate (NO3-), enabling the production of nitrous oxide (N2O, a potent greenhouse gas) by denitrification as a by-product (Canfield et al. 2010). Researchers at CIAT-Colombia in collaboration with JIRCAS-Japan, reported that Brachiaria humidicola forage grasses have the ability to inhibit the nitrification process by exuding chemical compounds from its roots to the soil. A major hydrophobic compound was discovered and named brachial-actone (Subbarao et al. 2009). This capacity of Brachiaria grasses is known as biological nitrification inhibition (BNI) and it could contribute to better N use efficiency in crop-livestock systems by improving recovery of applied N while reducing NO3- leaching and N2O emission. The current methodologies for quantifying the BNI trait need further improvement to facilitate high throughput evaluation to quantify genotypic differences. In this paper, we aim to develop new (or improve the existing) phenotyping methods for this trait. Preliminary results were obtained using three different methods to quantify BNI: (1) a mass spectrometry method to quantify brachialactone; (2) a static chamber method to quantify N2O emission from soils under greenhouse conditions; and (3) an improved molecular method to quantify microbial populations by Real-Time PCR. Using these three methods we expect to score a bi-parental hybrid population (n=134) of two B. humidicola accessions differing in their BNI capacity CIAT26146 (medium to low BNI) x CIAT16888 (high BNI), in an attempt to identify QTLs associated with the BNI trait

Nitrogen Management in Grasslands and Forage-Based Production Systems–Role of Biological Nitrification Inhibition (BNI)

Nitrogen (N), being the most critical and essential nutrient for plant growth, largely determines the productivity in both extensive- and intensive- grassland systems. Nitrification and denitrification processes in the soil are the primary drivers generating reactive-N: NO3-, N2O, and NO, and is largely responsible for N-loss and degradation of grasslands. Suppressing nitrification can thus facilitate the retention of soil-N to sustain long-term productivity of grasslands and forage-based production systems. Certain plants can suppress soil nitrification by releasing inhibitors from roots, a phenomenon termed ‘biological nitrification inhibition’ (BNI). Recent methodological developments (e.g. bioluminescence assay to detect BNIs from plant-root systems) led to significant advances in our ability to quantify and characterize BNI function in pasture grasses. Among grass-pastures, BNI-capacity is strongest in low-N adapted grasses such as Brachiaria humidicola and weakest in high-N environment grasses such as Italian ryegrass (Lolium perenne) and B. brizantha. The chemical identity of some of the BNIs produced in plant tissues and released from roots has now been established and their mode of inhibitory action determined on nitrifying bacteria Nitrosomonas. Synthesis and release of BNIs is a highly regulated and localized process, triggered by the presence of NH4+ in the rhizosphere, which facilitates the release of BNIs close to soil-nitrifier sites. Substantial genotypic variation is found for BNI-capacity in B. humidicola, which opens the way for its geneticmanipulation. Field studies suggest that Brachiaria grasses suppress nitrification and N2O emissions from soil. The potential for exploiting BNI function (from a genetic improvement and a system perspective) to develop production systems that are low-nitrifying, low N2O-emitting, economically efficient and ecologically sustainable, will be the subject of discussion

Fabrication of high quality plan-view TEM specimens using the focused ion beam

We describe a technique using a focused ion beam instrument to fabricate high quality plan-view specimens for transmission electron microscopy studies. The technique is simple, site-specific and is capable of fabricating multiple large, >100 μm2 electron transparent windows within epitaxially-grown thin films. A film of La0.67Sr0.33MnO3 is used to demonstrate the technique and its structural and functional properties are surveyed by high resolution imaging, electron spectroscopy, atomic force microscopy and Lorentz electron microscopy. The window is demonstrated to have good thickness uniformity and a low defect density that does not impair the film’s Curie temperature. The technique will enable the study of in–plane structural and functional properties of a variety of epitaxial thin film systems

Biological Nitrification Inhibition (BNI) in \u3cem\u3eBrachiaria\u3c/em\u3e Pastures: A Novel Strategy to Improve Eco-Efficiency of Crop-Livestock Systems and to Mitigate Climate Change

Up to 70% of the nitrogen (N) fertilizers applied to agricultural systems are lost due to nitrification and denitrification. Nitrification is a microbiological process that generates nitrate (NO3-) and promotes the losses of N fertilizers by leaching and denitrification. Nitrification and denitrification are the only known biological processes that generate nitrous oxide (N2O), a powerful greenhouse gas contributing to global warming. There is an urgent need to suppress nitrification process in soil to improve N-recovery and N use efficiency (NUE) of agricultural systems and to mitigate climate change (Subbarao et al. 2012). Certain Brachiaria grasses (B. humidicola) can suppress soil-nitrification by releasing biological nitrification inhibitors (BNIs) from roots, thereby reducing N2O emissions. This phenomenon, termed biological nitrification inhibition (BNI), has been the subject of recent research to characterize and validate the concept under field conditions (Subbarao et al. 2009). Advances on three aspects of BNI research are reported here: (1) gene quantification of soil nitrifying microorganisms to determine BNI activity in B. humidicola; (2) screening of B. humidicola breeding materials to identify hybrids with contrasting levels of BNI: and (3) quantification of the BNI-residual effect from B. humidicola on N-recovery and agronomic-NUE of the subsequent maize crop