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The new voices of science fiction
\"Your Future Is Bright! After all, your mother is a robot, your father has joined the alien hive mind, and your dinner will be counterfeit 3D-printed steak. Even though your worker bots have staged a mutiny, and your tour guide speaks only in memes, you can always sell your native language if you need some extra cash.\" -- From publisher's description.
Book
Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids
One of the largest contributions to biologically available nitrogen comes from the reduction of N₂ to ammonia by rhizobia in symbiosis with legumes. Plants supply dicarboxylic acids as a carbon source to bacteroids, and in return they receive ammonia. However, metabolic exchange must be more complex, because effective N₂ fixation by Rhizobium leguminosarum bv viciae bacteroids requires either one of two broad-specificity amino acid ABC transporters (Aap and Bra). It was proposed that amino acids cycle between plant and bacteroids, but the model was unconstrained because of the broad solute specificity of Aap and Bra. Here, we constrain the specificity of Bra and ectopically express heterologous transporters to demonstrate that branched-chain amino acid (LIV) transport is essential for effective N₂ fixation. This dependence of bacteroids on the plant for LIV is not due to their known down-regulation of glutamate synthesis, because ectopic expression of glutamate dehydrogenase did not rescue effective N₂ fixation. Instead, the effect is specific to LIV and is accompanied by a major reduction in transcription and activity of LIV biosynthetic enzymes. Bacteroids become symbiotic auxotrophs for LIV and depend on the plant for their supply. Bacteroids with aap bra null mutations are reduced in number, smaller, and have a lower DNA content than wild type. Plants control LIV supply to bacteroids, regulating their development and persistence. This makes it a critical control point for regulation of symbiosis.
Journal Article
Modeling agriculture in the Community Land Model
The potential impact of climate change on agriculture is uncertain. In addition, agriculture could influence above- and below-ground carbon storage. Development of models that represent agriculture is necessary to address these impacts. We have developed an approach to integrate agriculture representations for three crop types - maize, soybean, and spring wheat - into the coupled carbon-nitrogen version of the Community Land Model (CLM), to help address these questions. Here we present the new model, CLM-Crop, validated against observations from two AmeriFlux sites in the United States, planted with maize and soybean. Seasonal carbon fluxes compared well with field measurements for soybean, but not as well for maize. CLM-Crop yields were comparable with observations in countries such as the United States, Argentina, and China, although the generality of the crop model and its lack of technology and irrigation made direct comparison difficult. CLM-Crop was compared against the standard CLM3.5, which simulates crops as grass. The comparison showed improvement in gross primary productivity in regions where crops are the dominant vegetation cover. Crop yields and productivity were negatively correlated with temperature and positively correlated with precipitation, in agreement with other modeling studies. In case studies with the new crop model looking at impacts of residue management and planting date on crop yield, we found that increased residue returned to the litter pool increased crop yield, while reduced residue returns resulted in yield decreases. Using climate controls to signal planting date caused different responses in different crops. Maize and soybean had opposite reactions: when low temperature threshold resulted in early planting, maize responded with a loss of yield, but soybean yields increased. Our improvements in CLM demonstrate a new capability in the model - simulating agriculture in a realistic way, complete with fertilizer and residue management practices. Results are encouraging, with improved representation of human influences on the land surface and the potentially resulting climate impacts.
Journal Article
Modeling the impact of agricultural land use and management on US carbon budgets
Cultivation of the terrestrial land surface can create either a source or sink of atmospheric CO2, depending on land management practices. The Community Land Model (CLM) provides a useful tool for exploring how land use and management impact the soil carbon pool at regional to global scales. CLM was recently updated to include representation of managed lands growing maize, soybean, and spring wheat. In this study, CLM-Crop is used to investigate the impacts of various management practices, including fertilizer use and differential rates of crop residue removal, on the soil organic carbon (SOC) storage of croplands in the continental United States over approximately a 170-year period. Results indicate that total US SOC stocks have already lost over 8 Pg C (10%) due to land cultivation practices (e.g., fertilizer application, cultivar choice, and residue removal), compared to a land surface composed of native vegetation (i.e., grasslands). After long periods of cultivation, individual subgrids (the equivalent of a field plot) growing maize and soybean lost up to 65% of the carbon stored compared to a grassland site. Crop residue management showed the greatest effect on soil carbon storage, with low and medium residue returns resulting in additional losses of 5 and 3.5%, respectively, in US carbon storage, while plots with high residue returns stored 2% more carbon. Nitrogenous fertilizer can alter the amount of soil carbon stocks significantly. Under current levels of crop residue return, not applying fertilizer resulted in a 5% loss of soil carbon. Our simulations indicate that disturbance through cultivation will always result in a loss of soil carbon, and management practices will have a large influence on the magnitude of SOC loss.
Journal Article
A-trains for intraoperative monitoring in patients with recurrent vestibular schwannoma
Background
Second surgery of recurrent vestibular schwannoma (VS) after previous surgery, stereotactic radiosurgery (SR) or fractionated radiotherapy (FR) carries an increased risk for deterioration of facial nerve function, e.g., due to adhesions, underlining the need for intraoperative monitoring. Facial “A-train” EMG activity (“traintime”) correlates with the degree of postoperative facial palsy. Studies investigating A-trains in VS patients with previous surgery, SR or FR are missing. We therefore investigated the value of A-train monitoring in patients undergoing second surgery for VS.
Method
Intraoperative EMG data from patients who underwent second surgery for VS after previous surgery, SR and/or FR at our institution between 2006 and 2012 were retrospectively analyzed. Ten patients were selected (5 male): Seven had previous SR/RT and MS, three previous surgery only. Traintime values and distribution was compared to published thresholds and to 77 patients who underwent first surgery for VS during the same time period.
Results
A-trains were recorded early after opening of the dura, before facial nerve preparation. Mean traintime was 46.9 s (18.51 s – 80.82 s) in patients with previous SR/RT. In patients with previous MS only, traintime was 0.06 s, 0.99 s and 22.46 s. Compared to the literature, traintime was higher than expected in six patients (four with previous SR/RT, two without), respectively seven compared to the 77 patients with first surgery (5 SR/RT). Seven patients with previous SR/RT and none with previous surgery showed diffuse A-train distributions without significant percentages in single channels, compared to 60 of 77 patients with first surgery (
p
< 0.02).
Conclusions
Especially SR/RT, but also previous surgery seems to induce changes in the facial nerve leading to hyperexcitability and exceedingly high traintime values. Based on these findings, A-train monitoring in this specific patient group should be interpreted with caution.
Journal Article
The degradation of α-quaternary nonylphenol isomers by Sphingomonas sp. strain TTNP3 involves a type II ipso-substitution mechanism
The degradation of radiolabeled 4(3′,5′-dimethyl-3′-heptyl)-phenol [nonylphenol (NP)] was tested with resting cells of Sphingomonas sp. strain TTNP3. Concomitantly to the degradation of NP, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. Two other radiolabeled isomers of NP, 4(2′,6′-dimethyl-2′-heptyl)-phenol and 4(3′,6′-dimethyl-3′-heptyl)-phenol, were synthesized. In parallel experiments, the 4(2′,6′-dimethyl-2′-heptyl)-phenol was degraded more slowly than the other isomers of NP by strain TTNP3, possibly because of effects of the side-chain structure on the kinetics of degradation. Alkylbenzenediol and alkoxyphenol derivatives identified as metabolites during previous studies were synthesized and tested as substrates. The derivatives were not degraded, which indicated that the mineralization of NP does not proceed via alkoxyphenol as the principal intermediate. The results obtained led to the elucidation of the degradation pathway of NP isomers with a quaternary α-carbon. The proposed mechanism is a type II ipso substitution, leading to hydroquinone and nonanol as the main metabolites and to the dead-end metabolites alkylbenzenediol or alkoxyphenol, depending on the substitution at the α-carbon of the carbocationic intermediate formed.
Journal Article
Diversity of nifH gene amplified from rhizosphere soil DNA
Rhizosphere soils of chickpea (Cicer aeritinum) and wheat (Triticum aestivum) were analysed for the diversity of diazotrophic microorganisms by sequencing the nifH gene. A clone library of soil DNA amplified using highly degenerated nifH primers targeting the prokaryotic nitrogenase was constructed and subsequent RFLP analysis of nifH gene from clone libraries identified 28 and 25 genotypes in chickpea and wheat rhizosphere respectively. A total of 41 nifH genotypes were identified, out of which 12 were common in both rhizosphere soils. Sequencing of 41 nifH genotypes showed similarity to the corresponding genera of diazotrophs belonging to alpha, beta, gamma and delta proteobacteria. The prominent diazotrophs were Azospirillum brasilense, Bradyrhizobium spp., Azotobacter chroococcum, Methylococcus capsulatus, M. sylvestris, Sinorhizobium meliloti and Burkholderia vietnamenesis. A. brasilense was the dominant diazotroph present in the both rhizosphere soils. S. meliloti was only present in the chickpea rhizosphere, while B. vietnamanesis and Azoarcus tolulyticus were observed only in the wheat rhizosphere. The chickpea and wheat rhizospheres were diverse in diazotrophic bacterial community, as indicated by the occurrence of the nifH genotypes.
Journal Article
Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates
A group-specific primer set was developed using
nodC as a target gene for the amplification of rhizobial sequence diversity from nodule isolates and total soil DNA preparations. The primer set was tested on 209 nodule isolates, recovered from six different trap plant species which were grown in two soil samples collected from a chickpea and a wheat field site in India. We also amplified and cloned PCR products from total DNA isolated from the same soil samples. The total diversity within the resulting clone libraries (Σ 218 clones) was higher than that recovered from trap plants, but differed depending on the PCR protocols and primers used. However, some plant-selected genotypes could not be obtained using the community approach, probably due to variable detection limits and limited clone library sizes.
Journal Article
Interobserver variability of the House-Brackmann facial nerve grading system for the analysis of a randomized multi-center phase III trial
Background
Evidence of a high interobserver variability of the subjective House-Brackmann facial nerve grading system (HBGS) would justify cost- and time-consuming technological enhancements of objective classifications for facial nerve paresis.
Method
A total of 112 patients were recruited for a randomized multi-center trial to investigate the efficacy of prophylactic nimodipine treatment in vestibular schwannoma (VS) surgery. For the present investigation both treatment groups were pooled for the assessment of facial nerve function preoperatively, in the early postoperative course and 1 year after the surgery. Facial nerve function was documented photographically at rest and in motion and classified according to the HBGS by three independent observers (neurosurgeon, neurologist, ENT) and by the investigator of each center.
Results
Interobserver variability was considerably different with respect to the three time points depending upon the severity of facial nerve paresis. Preoperative facial nerve function was normal or only mildly impaired (HB grade I or II) and was assessed consistently in 97%. Facial nerve function deteriorated during the early postoperative course and was subsequently documented without dissent in only 36%, with one grade difference in 45%, two grade difference in 17% and three grade difference in 2%. One year after surgery, facial nerve function predominantly improved resulting in a consistent assessment in 66%. Differing ratings were observed in 34% with one grade deviation in 88% and of two grades in 12%. Patients with differing ratings of two or more grades exhibited considerably worse facial nerve function (p < 0.001).
Conclusions
The HBGS produced comparable results between different observers in patients with normal or only mildly impaired facial nerve function. Interobserver variability increased depending on the severity of facial nerve paresis. The results suggest that the HBGS does not promote uniformity of reporting and comparison of outcomes in patients with moderate or severe facial nerve paresis.
Journal Article