Axisymmetric theory and the interactive, asymmetric monsoon

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2005.Includes bibliographical references (p. 201-204).The applicability of axisymmetric theory of angular momentum conserving circulations to the large-scale steady monsoon is studied in a general circulation model with idealized representations of continental geometry and simple physics. The axisymmetric theory is expanded to explain the location of the monsoon; assuming quasi-equilibrium, the poleward boundary of the monsoon circulation will be collocated with the maximum in subcloud moist entropy, with the monsoon rains occurring slightly equatorward of this maximum. Starting from an axisymmetric aquaplanet framework, the model complexity is incrementally increased to include first a subtropical continent, then eddies and zonal variation in the flow, and finally asymmetry of the large-scale forcing. It is found that the meridional circulation which develops over a zonally symmetric continent is in good agreement with the axisymmetric theory, but a cross-equatorial meridional circulation does not form over a continent of limited longitudinal width, where the flow is highly asymmetric.(cont.) The equator proves to be a substantial barrier to boundary layer meridional flow; flow into the summer hemisphere from the winter hemisphere tends to occur in the free troposphere rather than in the boundary layer. The monsoon location is found to be strongly correlated with the maximum subcloud moist entropy, both in the modeled cases and in observed monsoons around the globe. The net effect of eddies is a slight weakening of the monsoon due to redistribution of the moist entropy field. Advection is found to strongly shape the overall distribution of subcloud moist entropy, and to limit the range of the monsoon circulation and precipitation.by Nikki C. Privé.Sc.D

Zonally symmetric monsoon dynamics in a general circulation model

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2002.Includes bibliographical references (p. 97-98).The MIT general circulation model is used with simplified setup to study steady zonally averaged monsoon circulations. Two dimensional model runs are made with a zonally symmetric continent north of 15N and a slab ocean of uniform sea surface temperature to study the applicability of axisymmetric theory. Forcing to drive the monsoon is applied by heating the subtropical land surface. The dynamical constraints of axisymmetry prevent low-level cross-equatorial flow and inhibit the northward transport of moisture onto the continent when there is no temperature gradient across the equator. The ocean cannot supply adequate moisture to feed the monsoon, and the ground hydrology strictly controls the behavior of the monsoon. A second set of two dimensional runs with similar continent, but with an SST gradient across the equator, result in a viable steady monsoon with low-level cross-equatorial flow providing moisture to the monsoon. The surface forcing required to induce a monsoon is reasonable given the constraints of the axisymmetric model setup. A series of three dimensional model runs with a zonally symmetric continent are made to study the role of zonally asymmetric flow on the zonal mean monsoon. It is found that greater land surface forcing is required to induce a zonally averaged monsoon circulation in the three dimensional runs than in similar axisymmetric runs. The behavior of the monsoon disturbances in the three dimensional runs is similar to the observed Asian monsoon in that there is low-level cross-equatorial flow which is southwesterly along the coastline, and in that a large-scale angular momentum conserving meridional circulation develops with ascent over the continent and subsidence in the opposite hemisphere. Moisture transport is found to play a very strong role in the monsoon dynamics in all of the model runs.by Nikki C. Privé.S.M

Molecular models should not be published without the corresponding atomic coordinates.

In PNAS, Romero et al. (1) present models of how glucocerebrosidase (GCase) interacts with saposin C (SAPC) and membranes. Unfortunately, the authors do not publish representative atomic coordinates or molecular dynamics trajectories for their models, denying researchers the opportunity to scrutinize the data Romero et al. (1) use to draw their functional conclusions. Access to these data is an important issue for structural biologists (2), and the open release of experimentally determined structural data has been the accepted practice for many years (3). Indeed, Romero et al. rely on several such publically available structures to carry out their study.J.E.D. is supported by a Royal Society University Research Fellowship (UF100371). S.C.G. is supported by a Sir Henry Dale Fellowship co-funded by the Royal Society and Wellcome Trust (098406/Z/12/B)

Identification and Characterization of Three Novel Lipases Belonging to Families II and V from Anaerovibrio lipolyticus 5ST

Following the isolation, cultivation and characterization of the rumen bacterium Anaerovibrio lipolyticus in the 1960s, it has been recognized as one of the major species involved in lipid hydrolysis in ruminant animals. However, there has been limited characterization of the lipases from the bacterium, despite the importance of understanding lipolysis and its impact on subsequent biohydrogenation of polyunsaturated fatty acids by rumen microbes. This study describes the draft genome of Anaerovibrio lipolytica 5ST, and the characterization of three lipolytic genes and their translated protein. The uncompleted draft genome was 2.83 Mbp and comprised of 2,673 coding sequences with a G+C content of 43.3%. Three putative lipase genes, alipA, alipB and alipC, encoding 492-, 438- and 248- amino acid peptides respectively, were identified using RAST. Phylogenetic analysis indicated that alipA and alipB clustered with the GDSL/SGNH family II, and alipC clustered with lipolytic enzymes from family V. Subsequent expression and purification of the enzymes showed that they were thermally unstable and had higher activities at neutral to alkaline pH. Substrate specificity assays indicated that the enzymes had higher hydrolytic activity against caprylate (C8), laurate (C12) and myristate (C14)

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome

Improving the health beneficial fatty acid content of meat and milk is a major challenge requiring an increased understanding of rumen lipid metabolism. In this study, we isolated and characterized rumen bacterial lipases/esterases using functional metagenomics. Metagenomic libraries were constructed from DNA extracted from strained rumen fluid (SRF), solid-attached bacteria (SAB) and liquid-associated rumen bacteria (LAB), ligated into a fosmid vector and subsequently transformed into an Escherichia coli host. Fosmid libraries consisted of 7,744; 8,448; and 7,680 clones with an average insert size of 30 to 35 kbp for SRF, SAB and LAB, respectively. Transformants were screened on spirit blue agar plates containing tributyrin for lipase/esterase activity. Five SAB and four LAB clones exhibited lipolytic activity, and no positive clones were found in the SRF library. Fosmids from positive clones were pyrosequenced and twelve putative lipase/esterase genes and two phospholipase genes retrieved. Although the derived proteins clustered into diverse esterase and lipase families, a degree of novelty was seen, with homology ranging from 40 to 78 % following BlastP searches. Isolated lipases/esterases exhibited activity against mostly short- to medium-chain substrates across a range of temperatures and pH. The function of these novel enzymes recovered in ruminal metabolism needs further investigation, alongside their potential industrial uses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-014-6355-6) contains supplementary material, which is available to authorized users

Robustness of Observing System Simulation Experiments

Observing System Simulation Experiments (OSSEs) are used to investigate the potential performance of proposed new instruments on numerical weather prediction (NWP). As OSSEs involve a framework in which the atmosphere and observations are all completely simulated, it is necessary to perform validation of the OSSE to ensure that it is sufficiently realistic to provide useful experimental results. A common issue that affects the forecast skill and observation impacts is the tendency of OSSEs to have insufficient model error compared to NWP in the real world. In this work, two versions of the National Aeronautics and Space Administration Global Modeling and Assimilation Office (NASA/GMAO) NWP OSSE framework are compared, with the newer framework having more simulated forecast model error than the older framework due to changes to the NWP system. The performance of the updated OSSE is validated against corresponding behavior of the same NWP system in the real world in terms of the simulated observations, the analysis increments, forecast error, and observation impacts. OSSE results of analysis and forecast impacts for three proposed new observation systems are also compared between the older and newer frameworks to evaluate the robustness of the OSSE experiments and the role of model error in observation impacts. These three new instruments are the Geostationary eXtended Observations (GeoXO) hyperspectral infrared sounder (GXS), the Midwave Infrared Sounding of Temperature and humidity in a Constellation for Winds (MISTiC Winds) atmospheric motion vectors, and additional Global Navigation Satellite System Radio Occultations (GNSS-RO)

Hotspots of Large Rare Deletions in the Human Genome

Background: We have examined the genomic distribution of large rare autosomal deletions in a sample of 440 parentparent-child trios from the Quebec founder population (QFP) which was recruited for a study of Attention Deficit Hyperactivity Disorder. Methodology/Principal Findings: DNA isolated from blood was genotyped on Illumina Hap300 arrays. PennCNV combined with visual evaluation of images generated by the Beadstudio program was used to determine deletion boundary definition of sufficient precision to discern independent events, with near-perfect concordance between parent and child in about 98 % of the 399 events detected in the offspring; the remaining 7 deletions were considered de novo. We defined several genomic regions of very high deletion frequency (‘hotspots’), usually of 0.4–0.6 Mb in length where independent rare deletions were found at frequencies of up to 100 fold higher than the average for the genome as a whole. Five of the 7 de novo deletions were in these hotspots. The same hotspots were also observed in three other studies on members of the QFP, those with schizophrenia, with endometriosis and those from a longevity cohort. Conclusions/Significance: Nine of the 13 hotspots carry one gene (7 of which are very long), while the rest contain no known genes. All nine genes have been implicated in disease. The patterns of exon deletions support the proposed roles for some of these genes in human disease, such as NRXN1 and PARKIN, and suggest limited roles or no role at all, for others

Buwchitin:A Ruminal Peptide with Antimicrobial Potential against <i>Enterococcus faecalis</i>

Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalispublishersversionPeer reviewe

PSMA-RLT in Patients with Metastatic Hormone-Sensitive Prostate Cancer : A Retrospective Study

Background: Prostate-specific membrane antigen (PSMA)-directed radioligand therapy (RLT) is a novel treatment for patients with castration-resistant prostate cancer (CRPC). Given the mode of action, patients in an earlier disease stage, such as hormone-sensitive prostate cancer (HSPC), are also likely to benefit from [177Lu]Lu-PSMA- (177Lu-PSMA) or [225Ac]Ac-PSMA-radioligand treatment (225Ac-PSMA). In this retrospective study, we analyzed the safety and efficacy of PSMARLT in early-stage and hormone-sensitive metastatic prostate cancer patients. Methods: A retrospective study was performed in patients who received 177Lu-PSMA and/or 225Ac-PSMA with early-stage metastatic prostate cancer. The primary outcome parameter evaluated in this study was the progression-free survival (PFS) after PSMA-RLT and toxicity according to the Common Terminology Criteria for Adverse Events. Secondary outcome parameters were prostate-specific antigen (PSA) response and the date of onset of CRPC state. Results: In total, 20 patients were included of which 18 patients received 177Lu-PSMA radioligand and two patients received tandem treatment with both 177Lu-PSMA and 225Ac-PSMA radioligands. Patients received a median of 2 treatment cycles (range 1–6) and a median activity of 6.2 GBq 177Lu-PSMA per cycle (interquartile range (IQR) 5.2–7.4 GBq). PSMA-RLT was overall well-tolerated. The most common grade 1–2 side effects were xerostomia (n = 6) and fatigue (n = 8), which were only temporarily reported. One patient that received 225Ac-PSMA developed grade 3–4 bone marrow toxicity. The median PFS was 12 months (95% confidence interval (CI), 4.09–19.9 months). Seventeen (85%) patients had a ≥50% PSA response following PSMA-RLT. One patient developed CRPC 9 months following PSMA-RLT. Conclusions: In this small cohort study, PSMA-RLT appeared safe and showed encouraging efficacy for (metastasized) early-stage and hormone-sensitive prostate cancer patients. Prospective studies are awaited and should include long-term follow-up