Developing Field-Sim: Software to support fieldwork

This case study provides an insight on how small-scale projects can be used to provide effective learning products. It examines the evolution of a project from the initial rationale, through the development process and onto subsequent evaluation and modification. It also provides a good example of how educational developers/technologists can work, in partnership with lecturers, to provide solutions to learning and teaching issue

Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum.

INTRODUCTION: Resistance to second-line tuberculosis drugs is common, but slow to diagnose with phenotypic drug sensitivity testing. Rapid molecular tests speed up diagnosis, but can only detect limited mutations. Whole genome sequencing (WGS) of culture isolates can generate a complete genetic drug resistance profile, but is delayed by the initial culture step. In the case presented here, successful WGS directly from sputum was achieved using targeted enrichment. CASE REPORT: A 29-year-old Nigerian woman was diagnosed with tuberculosis. Xpert MTB/RIF and Hain line probe assays identified rpoB and inhA mutations consistent with rifampicin and intermediate isoniazid resistance, and a further possible mutation conferring fluoroquinolone resistance. WGS directly from sputum identified a further inhA mutation consistent with high-level isoniazid resistance and confirmed the absence of fluoroquinolone resistance. Isoniazid was stopped, and the patient has completed 18 months of a fluoroquinolone-based regimen without relapse. DISCUSSION: Compared to rapid molecular tests (which can only examine a limited number of mutations) and WGS of culture isolates (which requires a culture step), WGS directly from sputum can quickly generate a complete genetic drug resistance profile. In this case, WGS altered the clinical management of drug-resistant tuberculosis and demonstrated potential for guiding individualized drug treatment where second-line drug resistance is common

Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.

We report results of a nonsynonymous SNP scan for ulcerative colitis and identify a previously unknown susceptibility locus at ECM1. We also show that several risk loci are common to ulcerative colitis and Crohn's disease (IL23R, IL12B, HLA, NKX2-3 and MST1), whereas autophagy genes ATG16L1 and IRGM, along with NOD2 (also known as CARD15), are specific for Crohn's disease. These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases

Lunar magnetism

Analyses of lunar rocks and magnetic field data from orbit show that the Moon once had a global magnetic field generated by an internal dynamo. Magnetization of the deep crust implies that a dynamo operated during the first 100 million years following crust formation and magnetization of some impact basins implies that the dynamo continued into the Nectarian period. Paleomagnetic analyses of Apollo samples provide evidence for dynamo activity from about 4.25 billion years ago (Ga) until at least 1.92 Ga, ceasing thereafter by ~0.80 Ga. The field strength was Earth-like until about 3.56 Ga (from ~40 to 110 μT), after which it decreased by more than an order of magnitude. Several mechanisms have been proposed to account for the long duration of the lunar dynamo. These include thermal convection in the core that could power a dynamo for a few hundred million years, core crystallization that could power a dynamo until about 1.5 Ga, mantle and/or inner core precession that could power a dynamo beyond 2 Ga, impact-induced changes in the rotation rate of the mantle that could power several short-lived dynamos up until when the last basin formed at ~3.7 Ga, and a basal magma ocean that could have potentially powered a dynamo over much of lunar history. Magnetohydrodynamic simulations have shown that the amplification of pre-existing fields by impact generated plasmas are insufficient and too short lived to have played an important role in crustal magnetization. Some of the magnetic carriers responsible for crustal magnetization, such as those responsible for the magnetization of the deep highland crust and mare basalts, are of lunar origin. Other magnetic carriers may instead be derived from meteoritic materials that were accreted to the Moon during large impacts. Outstanding questions in lunar magnetism include the geometry of the internally generated magnetic field, the exceedingly high surface field strengths implied by some paleomagnetic analyses, whether dynamo activity was continuous or episodic, the origin of strong crustal magnetic anomalies that have no correlation with surface geology, and the mechanisms that powered the lunar dynamo through time

Lunar magnetism

Analyses of lunar rocks and magnetic field data from orbit show that the Moon once had a global magnetic field generated by an internal dynamo. Magnetization of the deep crust implies that a dynamo operated during the first 100 million years following crust formation and magnetization of some impact basins implies that the dynamo continued into the Nectarian period. Paleomagnetic analyses of Apollo samples provide evidence for dynamo activity from about 4.25 billion years ago (Ga) until at least 1.92 Ga, ceasing thereafter by ~0.80 Ga. The field strength was Earth-like until about 3.56 Ga (from ~40 to 110 μT), after which it decreased by more than an order of magnitude. Several mechanisms have been proposed to account for the long duration of the lunar dynamo. These include thermal convection in the core that could power a dynamo for a few hundred million years, core crystallization that could power a dynamo until about 1.5 Ga, mantle and/or inner core precession that could power a dynamo beyond 2 Ga, impact-induced changes in the rotation rate of the mantle that could power several short-lived dynamos up until when the last basin formed at ~3.7 Ga, and a basal magma ocean that could have potentially powered a dynamo over much of lunar history. Magnetohydrodynamic simulations have shown that the amplification of pre-existing fields by impact generated plasmas are insufficient and too short lived to have played an important role in crustal magnetization. Some of the magnetic carriers responsible for crustal magnetization, such as those responsible for the magnetization of the deep highland crust and mare basalts, are of lunar origin. Other magnetic carriers may instead be derived from meteoritic materials that were accreted to the Moon during large impacts. Outstanding questions in lunar magnetism include the geometry of the internally generated magnetic field, the exceedingly high surface field strengths implied by some paleomagnetic analyses, whether dynamo activity was continuous or episodic, the origin of strong crustal magnetic anomalies that have no correlation with surface geology, and the mechanisms that powered the lunar dynamo through time

Lunar Magnetism

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