Nitrogen loss (NH3, N2O) patterns in bench-scale composting.

Nitrogen (N) losses during composting reduce the value of the end product as a fertilizer. Nitrogen is lost during composting mainly by ammonia (NH3) volatilization in the thermophilic phase. We used three bench-scale aerobic bioreactors with a controlled temperature difference (CDT) system as an experimental approach to investigate the pattern of N losses during composting. N2O peak emission occurred much earlier (7h) than NH3 volatilization (48-60h) during the thermophilic phase (~55°C) of bench-scale composting. The NH3 volatilization peak rate occurred following the greater biological activity (O2 consumed/CO2 evolved) at 40°C which could coincide with greater ammonification, but immobilization of NH4+/NH3 also occurs at this point affecting NH3 volatilization. Differences in temperature curves and accumulated NH3-N were related to the biological activity in each vessel. Therefore, O2 consumed/CO2 evolved measurements must be part of the evaluation of composting in further studies for comparisons of techniques to reduce NH3 volatilizatio

Insensitivity of alkenone carbon isotopes to atmospheric CO₂ at low to moderate CO₂ levels

Atmospheric pCO2 is a critical component of the global carbon system and is considered to be the major control of Earth’s past, present and future climate. Accurate and precise reconstructions of its concentration through geological time are, therefore, crucial to our understanding of the Earth system. Ice core records document pCO2 for the past 800 kyrs, but at no point during this interval were CO2 levels higher than today. Interpretation of older pCO2 has been hampered by discrepancies during some time intervals between two of the main ocean-based proxy methods used to reconstruct pCO2: the carbon isotope fractionation that occurs during photosynthesis as recorded by haptophyte biomarkers (alkenones) and the boron isotope composition (δ11B) of foraminifer shells. Here we present alkenone and δ11B-based pCO2 reconstructions generated from the same samples from the Plio-Pleistocene at ODP Site 999 across a glacial-interglacial cycle. We find a muted response to pCO2 in the alkenone record compared to contemporaneous ice core and δ11B records, suggesting caution in the interpretation of alkenone-based records at low pCO2 levels. This is possibly caused by the physiology of CO2 uptake in the haptophytes. Our new understanding resolves some of the inconsistencies between the proxies and highlights that caution may be required when interpreting alkenone-based reconstructions of pCO2

Historical trends in pH and carbonate biogeochemistry on the Belize Mesoamerican barrier reef system

Coral reefs are important ecosystems that are increasingly negatively impacted by human activities. Understanding which anthropogenic stressors play the most significant role in their decline is vital for the accurate prediction of future trends in coral reef health and for effective mitigation of these threats. Here we present annually resolved boron and carbon isotope measurements of two cores capturing the past 90 years of growth of the tropical reef‐building coral Siderastrea siderea from the Belize Mesoamerican Barrier Reef System. The pairing of these two isotope systems allows us to parse the reconstructed pH change into relative changes in net ecosystem productivity and net ecosystem calcification between the two locations. This approach reveals that the relationship between seawater pH and coral calcification, at both a colony and ecosystem level, is complex and cannot simply be modeled as linear or even positive. This study also underscores both the utility of coupled δ11B‐δ13C measurements in tracing past biogeochemical cycling in coral reefs and the complexity of this cycling relative to the open ocean

Disease-specific, neurosphere-derived cells as models for brain disorders

There is a pressing need for patient-derived cell models of brain diseases that are relevant and robust enough to produce the large quantities of cells required for molecular and functional analyses. We describe here a new cell model based on patient-derived cells from the human olfactory mucosa, the organ of smell, which regenerates throughout life from neural stem cells. Olfactory mucosa biopsies were obtained from healthy controls and patients with either schizophrenia, a neurodevelopmental psychiatric disorder, or Parkinson's disease, a neurodegenerative disease. Biopsies were dissociated and grown as neurospheres in defined medium. Neurosphere-derived cell lines were grown in serum-containing medium as adherent monolayers and stored frozen. By comparing 42 patient and control cell lines we demonstrated significant disease-specific alterations in gene expression, protein expression and cell function, including dysregulated neurodevelopmental pathways in schizophrenia and dysregulated mitochondrial function, oxidative stress and xenobiotic metabolism in Parkinson's disease. The study has identified new candidate genes and cell pathways for future investigation. Fibroblasts from schizophrenia patients did not show these differences. Olfactory neurosphere-derived cells have many advantages over embryonic stem cells and induced pluripotent stem cells as models for brain diseases. They do not require genetic reprogramming and they can be obtained from adults with complex genetic diseases. They will be useful for understanding disease aetiology, for diagnostics and for drug discovery

Improvement in Chronic Hepatocerebral Degeneration Following Liver Transplantation

Chronic progressive hepatocerebral degeneration with spastic paraparesis, dementia, dysarthria, ataxia, tremor, and neuropsychiatric symptoms follows long-standing portal-systemic shunting, is associated with structural changes in the central nervous system, and does not respond to conventional therapy for hepatic encephalopathy. A case of advanced chronic liver disease with severe, progressive hepatocerebral degeneration after 23 yr of portal-systemic shunting is reported in whom there was significant objective improvement in intellectual function and in the chronic neurological signs 3 mo after orthotopic liver transplantation and further improvement 12 mo after transplantation

Size-dependent response of foraminiferal calcification to seawater carbonate chemistry

Michael J. Henehan acknowledges financial support from the Yale Peabody Museum.The response of the marine carbon cycle to changes in atmospheric CO2 concentrations will be determined, in part, by the relative response of calcifying and non-calcifying organisms to global change. Planktonic foraminifera are responsible for a quarter or more of global carbonate production, therefore understanding the sensitivity of calcification in these organisms to environmental change is critical. Despite this, there remains little consensus as to whether, or to what extent, chemical and physical factors affect foraminiferal calcification. To address this, we directly test the effect of multiple controls on calcification in culture experiments and core-top measurements of Globigerinoides ruber. We find that two factors, body size and the carbonate system, strongly influence calcification intensity in life, but that exposure to corrosive bottom waters can overprint this signal post mortem. Using a simple model for the addition of calcite through ontogeny, we show that variable body size between and within datasets could complicate studies that examine environmental controls on foraminiferal shell weight. In addition, we suggest that size could ultimately play a role in determining whether calcification will increase or decrease with acidification. Our models highlight that knowledge of the specific morphological and physiological mechanisms driving ontogenetic change in calcification in different species will be critical in predicting the of foraminiferal calcification to future change in atmospheric pCO2.Publisher PDFPeer reviewe

Cronkhite-Canada Syndrome Associated with Peripheral Neuropathy

Here we report a patient with Cronkhite-Canada Syndrome and peripheral neuropathy, a previously unreported association

Sensorimotor Peripheral Neuropathy in Rheumatoid Arthritis

We describe three patients with severe sensorimotor neuropathy complicating rheumatoid arthritis. Two patients had evidence of vasculitis and an axonal neuropathy. These patients were unusual in that the neuropathy occurred early in the course of rheumatoid arthritis. The third patient had a demyelinating neuropathy with a high cerebrospinal fluid protein level, and is a probable example of a chronic inflammatory neuropathy occurring in rheumatoid arthritis. All patients improved or were stabilized with corticosteroid therapy

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect

<p>Abstract</p> <p>Background</p> <p>RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value.</p> <p>Results</p> <p>We present siDirect 2.0, an update of our web-based software siDirect, which provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5°C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects.</p> <p>Conclusion</p> <p>siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5°C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in RefSeq. siDirect 2.0 is available at <url>http://siDirect2.RNAi.jp/</url>.</p

Binding MOAD, a high-quality protein–ligand database

Binding MOAD (Mother of All Databases) is a database of 9836 protein–ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the protein–ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org