Coupled afterslip and transient mantle flow after the 2011 Tohoku earthquake.

Modeling of postseismic deformation following great earthquakes has revealed the viscous structure of the mantle and the frictional properties of the fault interface. However, for giant megathrust events, viscoelastic flow and afterslip mechanically interplay with each other during the postseismic period. We explore the role of afterslip and viscoelastic relaxation and their interaction in the aftermath of the 2011 M w (moment magnitude) 9.0 Tohoku earthquake based on a detailed model analysis of the postseismic deformation with laterally varying, experimentally constrained, rock rheology. Mechanical coupling between viscoelastic relaxation and afterslip notably modifies both the afterslip distribution and surface deformation. Thus, we highlight the importance of addressing mechanical coupling for long-term studies of postseismic relaxation, especially in the context of the geodynamics of the Japan trench across the seismic cycle.

A Medium-Throughput Single Cell CRISPR-Cas9 Assay to Assess Gene Essentiality.

BACKGROUND: Target selection for oncology is a crucial step in the successful development of therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 editing of specific loci offers an alternative method to RNA interference and small molecule inhibitors for determining whether a cell line is dependent on a specific gene product for proliferation or survival. In our initial studies using CRISPR-Cas9 to verify the dependence on EZH2 activity for proliferation of a SMARCB1/SNF5/INI1 mutant malignant rhabdoid tumor (MRT) cell line, we noted that the initial reduction in proliferation was lost over time. We hypothesized that in the few cells that retain proliferative capacity, at least one allele of EZH2 remains functional. To verify this, we developed an assay to analyze 10s-100s of clonal cell populations for target gene disruption using restriction digest and fluorescent fragment length analyses. RESULTS: Our results clearly show that in cell lines in which EZH2 is essential for proliferation, at least one potentially functional allele of EZH2 is retained in the clones that survive. CONCLUSION: This assay clearly indicates whether or not a specific gene is essential for survival and/or proliferation in a given cell line. Such data can aid the development of more robust therapeutics by increasing confidence in target selection.

Tree species partition N uptake by soil depth in boreal forests.

It is recognized that the coexistence of herbaceous species in N-depleted habitats can be facilitated by N partitioning; however, the existence of such a phenomenon for trees has not yet been demonstrated. Here, we show from both foliage and soil 15N natural abundance values and from a 12-year in situ 15N addition experiment, that black spruce (Picea mariana) and jack pine (Pinus banksiana), two widespread species of the Canadian boreal forest, take up N at different depths. While black spruce takes up N from the organic soil, jack pine acquires it deeper within the highly N-depleted mineral soil. Systematic difference in foliar 15N natural abundance between the two species across seven sites distributed throughout the eastern Canadian boreal forest shows that N spatial partitioning is a widespread phenomenon. Distinct relationships between delta15N and N concentration in leaves of both species further emphasize their difference in N acquisition strategies. This result suggests that such complementary mechanisms of N acquisition could facilitate tree species coexistence in such N-depleted habitats and could contribute to the positive biodiversity-productivity relationship recently revealed for the eastern Canadian boreal forest, where jack pine is present. It also has implications for forest management and provides new insights to interpret boreal forest regeneration following natural or anthropogenic perturbations.

A scanning Hall probe imaging study of the field induced martensite-austenite phase transition in Ni50Mn34In16 alloy.

The martensite to austenite phase transition in the off-stoichiometric Heusler alloy Ni(50)Mn(34)In(16) can be induced both by temperature change and by application of a magnetic field. We have used scanning Hall probe imaging to study the magnetic field induced martensite-austenite phase transition. The study provides clear visual evidence of the coexistence of the martensite and austenite phases across this field induced transition in both increasing and decreasing magnetic fields. Clear evidence of thermomagnetic history effects associated with the martensite-austenite phase transition is also obtained. Quantitative analysis of the magnetic field dependence of the volume fraction of the austenite phase in Ni(50)Mn(34)In(16) shows evidence of a nucleation and growth mechanism across the field induced martensite-austenite phase transition. The local M-H loops constructed from the Hall images indicate the presence of a landscape of the critical magnetic field (for the field induced transition) distributed over the sample volume and thus confirm the disorder influenced nature of this first-order magnetic phase transition.

Coexistence of universal and topological anomalous hall effects in metal CrO2 thin films in the dirty limit.

The scaling exponent of 1.6 between anomalous Hall and longitudinal conductivity, characteristic of the universal Hall mechanism in dirty-metal ferromagnets, emerges from a series of CrO2 films as we systematically increase structural disorder. Magnetic disorder in CrO2 increases with temperature and this drives a separate topological Hall mechanism. We find that these terms are controlled discretely by structural and magnetic defect populations, and their coexistence leads to apparent divergence from exponent 1.6, suggesting that the universal term is more prevalent than previously realized.

Heat capacity and latent heat measurements of CoMnSi using a microcalorimeter.

A new method of utilizing a commercial silicon nitride membrane calorimeter to measure the latent heat at a first order phase transition is presented. The method is a direct measurement of the thermoelectric voltage jump induced by the latent heat, in a thermally isolated system ideally suited for single crystal and small microgram samples. We show that when combined with the ac calorimetry technique previously developed, the resultant thermal measurement capabilities are extremely powerful. We demonstrate the applicability of the combined method with measurements on a 100 microm size fragment of CoMnSi exhibiting a sizable magnetocaloric effect near room temperature, and obtain good agreement with previously reported values on bulk samples.

TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism.

SUMMARY: TreeMos is a novel high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences. TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualizes instances of sequence segments whose nearest neighbour is anomalous to that identified using the global alignment. Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome. TreeMos can be run from the command line, or within a web browser allowing the relationships between taxa to be explored by drill-through. AVAILABILITY: http://www2.warwick.ac.uk/fac/sci/whri/research/archaeobotany.

Expression of membrane proteins from Mycobacterium tuberculosis in Escherichia coli as fusions with maltose binding protein.

Sixteen of 22 low molecular weight integral membrane proteins from Mycobacterium tuberculosis with previously poor or undetectable levels of expression were expressed in Escherichia coli as fusions with both the maltose binding protein (MBP) and a His(8)-tag. Sixty-eight percent of targeted proteins were expressed in high yield (>30 mg/L) in soluble and/or inclusion body form. Thrombin cleavage of the MBP fusion protein was successful for 10 of 13 proteins expressed as soluble proteins and for three proteins expressed only as inclusion bodies. The use of autoinduction growth media increased yields over Luria-Bertani (LB) growth media in 75% of the expressed proteins. Expressing integral membrane proteins with yields suitable for structural studies from a set of previously low and non-expressing proteins proved highly successful upon attachment of the maltose binding protein as a fusion tag.

Depression and dysthymia.

The advances made in the 1980s and 1990s have yielded many advances in the diagnosis and treatment of depression and dysthymia. Skill of the clinician is important in sorting out the diagnosis, taking care to consider the various medical conditions that can cause depression or disguise themselves as depression. Depressive disorders are highly treatable conditions. Clinicians must overcome the stigma associated with these disorders to alleviate the pain and suffering of those afflicted. The advances in treatment have been enormous and continue to grow. The keys to these treatments lie in continuing to acquire the knowledge to unlock all of the causes of depression. An appendix follows listing medications commonly used in the treatment of depression or for other conditions in patients under treatment for depression.

The Ran-GTPase and cell-cycle control.

RCC1, the chromatin-bound guanine-nucleotide exchange factor (GEF) for the small nuclear GTPase, Ran, is required for coordinating the onset of mitosis with S-phase completion in mammalian cells. Other defects in the Ran-GTPase network also result in disruption of cell-cycle processes such as DNA replication, exit from mitosis and, at least in budding yeast, accurate chromosome segregation. However, the Ran system is now best known for its pivotal role in nucleocytoplasmic transport, where RanGTP is used as a positional flag for the nucleus during interphase. Ran's effectors are the shuttling transport factors, importins and exportins, which facilitate the transit of cargoes between the nucleus and cytoplasm: RanGTP regulates their cargo-binding properties so that they can move their cargo in the correct direction. RanGTP also plays a separate role during mitosis, influencing microtubule polymerisation, possibly specifically in the vicinity of chromosomes. Most recently, Ran has been shown to be crucial for the regeneration of a nuclear envelope after exit from mitosis. So, can the problems with cell-cycle progression and control induced by perturbing the Ran-system be attributed to defects in these three processes? This article examines this issue, concentrating on vertebrate systems. BioEssays 23:77-85, 2001.

Simultaneous quantitation of the 5'-triphosphate metabolites of zidovudine, lamivudine, and stavudine in peripheral mononuclear blood cells of HIV infected patients by high-performance liquid chromatography tandem mass spectrometry.

A high-performance liquid chromatography (HPLC) method utilizing triple quadrupole mass spectrometry (MS) detection was developed and validated for the simultaneous measurement of the intracellular nucleoside 5'-triphosphate anabolites of zidovudine (ZDV-TP), lamivudine (3TC-TP), and stavudine (d4T-TP). These compounds were extracted from patient peripheral blood mononuclear cells (PBMCs) which are the sites of HIV replication and drug action. Ion-exchange solid phase extraction (SPE) followed by enzymatic digestion with alkaline phosphatase was utilized to yield the measurable nucleoside forms of the nucleotides. Reversed phase C-18 SPE with addition of a nucleoside internal standard, 3'-azido-2',3'-dideoxyuridine (AzdU) allowed for the indirect measurement of the original 5'-triphosphate concentration by HPLC/MS/MS. Quantitation was performed from calibration curves generated from authentic 5'-triphosphate standards spiked in PBMCs from healthy volunteers. Analytical range for the three 5'-triphosphates was equivalent to 50-45,000 pg. Mean interassay accuracies for 3TC-TP, d4T-TP, and ZDV-TP (n > 90) were 99.4%, 100.1%, and 108.0%, respectively. Mean interassay precisions (%C.V.) for 3TC-TP, d4T-TP, and ZDV-TP (n > 90) were 8.8%, 10.4%, and 8.2%, respectively. Recovery of the extraction method was 79.2%, 83.1%, and 98.3% for 3TC-TP, d4T-TP, and ZDV-TP, respectively. This method can be utilized to measure the intracellular 5'-triphosphate levels in HIV infected patients receiving antiretroviral therapy containing the nucleoside reverse transcriptase inhibitors 3TC, d4T, or ZDV.

System divorces on rise. Unscrambling deals is messy and contentious.

The mass merger movement of the 1990s has hit the wall. More and more systems are taking a hard look at what their expensive deals have wrought, and are finding they don't like what they see. Disbanding systems are facing messy problems, and there are many questions as to whether de-merged hospitals can make it on their own.

Phase I dose escalation pharmacokinetics of O-(chloroacetylcarbamoyl) fumagillol (TNP-470) and its metabolites in AIDS patients with Kaposi's sarcoma.

The pharmacokinetics of TNP-470 and its major metabolites were investigated in AIDS patients enrolled in a phase I dose escalation trial for the treatment of Kaposi's sarcoma. The patients received TNP-470 by 1-h intravenous infusion in dose cohorts of 10, 20, 30, 40, 50 and 70 mg/m2. The parent drug and metabolites, MII and MIV, were measured by high-performance liquid chromatography/mass spectrometry (HPLC/MS) in plasma samples collected during and out to 168 h after the beginning of the infusion. Both metabolites were detected in all patients' plasma, while the parent drug was undetectable at time-points as early as 5 min after the end of infusion for some patients. A large interpatient variability of pharmacokinetic parameters among the dosing cohorts was observed for TNP-470, with a mean (+/- SD) plasma elimination half-life (t1/2) of 0.06 +/- 0.04 h, plasma clearance (CL) of 1487 +/- 1216 l/h and an area under the concentration versus time curve (AUC) of 49.9 +/- 35.8 ng/ml x h. Time to maximum plasma concentration (Tmax) typically occurred before the end of the infusion. The predominant plasma metabolite was MII with a t1/2 of 1.21 +/- 0.43 h, AUC of 1226 +/- 2303 l/h and a Tmax occurring between 5 and 15 min after infusion. The reported active metabolite MIV had a t1/2 of 0.24 +/- 0.13 h, AUC of 24.9 +/- 32.6 ng/ml x h and a Tmax occurring between the midpoint of the infusion and 15 min after infusion. The parent drug was undetectable by HPLC/MS/MS in urine samples collected and pooled between 0-6 and 6-24 h from the beginning of drug administration. Metabolite MIV was present in the 0-6-h urine pool of two patients enrolled in the highest dosing cohorts, equivalent to 0.4% of the administered dose. Metabolite MII was present in all 0-6-h samples analyzed and represented 1.12 +/- 0.9% of the administered dose. Renal clearance (CLR) for MII was 140 +/- 70 ml/h.