Variants in Bedaquiline-Candidate-Resistance Genes: Prevalence in Bedaquiline-Naive Patients, Effect on MIC, and Association with Mycobacterium tuberculosis Lineage.

Studies have shown that variants in bedaquiline-resistance genes can occur in isolates from bedaquiline-naive patients. We assessed the prevalence of variants in all bedaquiline-candidate-resistance genes in bedaquiline-naive patients, investigated the association between these variants and lineage, and the effect on phenotype. We used whole-genome sequencing to identify variants in bedaquiline-resistance genes in isolates from 509 bedaquiline treatment naive South African tuberculosis patients. A phylogenetic tree was constructed to investigate the association with the isolate lineage background. Bedaquiline MIC was determined using the UKMYC6 microtiter assay. Variants were identified in 502 of 509 isolates (98.6%), with the highest (85%) prevalence of variants in the Rv0676c (mmpL5) gene. We identified 36 unique variants, including 19 variants not reported previously. Only four isolates had a bedaquiline MIC equal to or above the epidemiological cut-off value of 0.25 µg/mL. Phylogenetic analysis showed that 14 of the 15 variants observed more than once occurred monophyletically in one Mycobacterium tuberculosis (sub)lineage. The bedaquiline MIC differed between isolates belonging to lineage 2 and 4 (Fisher's exact test, P = 0.0004). The prevalence of variants in bedaquiline-resistance genes in isolates from bedaquiline-naive patients is high, but very few (<2%) isolates were phenotypically resistant. We found an association between variants in bedaquiline resistance genes and Mycobacterium tuberculosis (sub)lineage, resulting in a lineage-dependent difference in bedaquiline phenotype. Future studies should investigate the impact of the presence of variants on bedaquiline-resistance acquisition and treatment outcome.

Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data.

The study of genetic minority variants is fundamental to the understanding of complex processes such as evolution, fitness, transmission, virulence, heteroresistance and drug tolerance in Mycobacterium tuberculosis (Mtb). We evaluated the performance of the variant calling tool LoFreq to detect de novo as well as drug resistance conferring minor variants in both in silico and clinical Mtb next generation sequencing (NGS) data. The in silico simulations demonstrated that LoFreq is a conservative variant caller with very high precision (≥96.7%) over the entire range of depth of coverage tested (30x to1000x), independent of the type and frequency of the minor variant. Sensitivity increased with increasing depth of coverage and increasing frequency of the variant, and was higher for calling insertion and deletion (indel) variants than for single nucleotide polymorphisms (SNP). The variant frequency limit of detection was 0.5% and 3% for indel and SNP minor variants, respectively. For serial isolates from a patient with DR-TB; LoFreq successfully identified all minor Mtb variants in the Rv0678 gene (allele frequency as low as 3.22% according to targeted deep sequencing) in whole genome sequencing data (median coverage of 62X). In conclusion, LoFreq can successfully detect minor variant populations in Mtb NGS data, thus limiting the need for filtering of possible false positive variants due to sequencing error. The observed performance statistics can be used to determine the limit of detection in existing whole genome sequencing Mtb data and guide the required depth of future studies that aim to investigate the presence of minor variants.

Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.

The next-generation, short-read sequencing technologies that generate comprehensive, whole-genome data with single nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance, and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long-read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data are available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.

Patched Local Lunar Gravity Solutions Using GRAIL Data.

We present a method to determine local gravity fields for the Moon using Gravity Recovery and Interior Laboratory (GRAIL) data. We express gravity as gridded gravity anomalies on a sphere, and we estimate adjustments to a background global start model expressed in spherical harmonics. We processed GRAIL Ka-band range-rate data with a short-arc approach, using only data over the area of interest. We determine our gravity solutions using neighbor smoothing constraints. We divided the entire Moon into 12 regions and 2 polar caps, with a resolution of 0.15 ° × 0.15 ° (which is equivalent to degree and order 1199 in spherical harmonics), and determined the optimal smoothing parameter for each area by comparing localized correlations between gravity and topography for each solution set. Our selected areas share nodes with surrounding areas and they are overlapping. To mitigate boundary effects, we patch the solutions together by symmetrically omitting the boundary parts of overlapping solutions. Our new solution has been iterated, and it has improved correlations with topography when compared to a fully iterated global model. Our method requires fewer resources, and can easily handle regionally varying resolution or constraints. The smooth model describes small-scale features clearly, and can be used in local studies of the structure of the lunar crust.

Mechanisms of Drug-Induced Tolerance in Mycobacterium tuberculosis.

Successful treatment of tuberculosis (TB) can be hampered by Mycobacterium tuberculosis populations that are temporarily able to survive antibiotic pressure in the absence of drug resistance-conferring mutations, a phenomenon termed drug tolerance. We summarize findings on M. tuberculosis tolerance published in the past 20 years. Key M. tuberculosis responses to drug pressure are reduced growth rates, metabolic shifting, and the promotion of efflux pump activity. Metabolic shifts upon drug pressure mainly occur in M. tuberculosis's lipid metabolism and redox homeostasis, with reduced tricarboxylic acid cycle activity in favor of lipid anabolism. Increased lipid anabolism plays a role in cell wall thickening, which reduces sensitivity to most TB drugs. In addition to these general mechanisms, drug-specific mechanisms have been described. Upon isoniazid exposure, M. tuberculosis reprograms several pathways associated with mycolic acid biosynthesis. Upon rifampicin exposure, M. tuberculosis upregulates the expression of its drug target rpoB Upon bedaquiline exposure, ATP synthesis is stimulated, and the transcription factors Rv0324 and Rv0880 are activated. A better understanding of M. tuberculosis's responses to drug pressure will be important for the development of novel agents that prevent the development of drug tolerance following treatment initiation. Such agents could then contribute to novel TB treatment-shortening strategies.

Improving the geometry of Kaguya extended mission data through refined orbit determination using laser altimetry.

The Japan Aerospace Exploration Agency's (JAXA) Kaguya spacecraft carried a suite of instruments to map the Moon and its environment globally. During its extended mission, the average altitude was 50 km or lower, and Kaguya science products using these data hence have an increased spatial resolution. However, the geodetic position quality of these products is much worse than that of those acquired during the primary mission (at an altitude of 100 km) because of reduced radiometric tracking and frequent thrusting to maintain spacecraft attitude after the loss of momentum wheels. We have analyzed the Kaguya tracking data using gravity models based on the Gravity Recovery and Interior Laboratory (GRAIL) mission, and by making use of a new data type based on laser altimeter data collected by Kaguya: we adjust the spacecraft orbit such that the altimetry tracks fit a precise topographic basemap based on the Lunar Reconnaissance Orbiter's (LRO) Lunar Orbiter Laser Altimeter (LOLA) data. This results in geodetically accurate orbits tied to the precise LOLA/LRO frame. Whereas previously archived orbits show errors at the level of several a level of several tens of meters. When altimetry data are not available, the combination of GRAIL gravity and radio tracking results in an orbit precision of around several hundreds of meters for the low-altitude phase of the extended mission. Our greatly improved orbits result in better geolocation of the Kaguya extended mission data set.

Geodetic evidence that Mercury has a solid inner core.

Geodetic analysis of radio tracking measurements of the MESSENGER spacecraft while in orbit about Mercury has yielded new estimates for the planet's gravity field, tidal Love number, and pole coordinates. The derived right ascension (α = 281.0082° ± 0.0009°; all uncertainties are 3 standard deviations) and declination (δ =61.4164° ± 0.0003°) of the spin pole place Mercury in the Cassini state. Confirmation of the equilibrium state with an estimated mean (whole-planet) obliquity ϵ of 1.968 ± 0.027 arcmin enables the confident determination of the planet's normalized polar moment of inertia (0.333 ± 0.005), which indicates a high degree of internal differentiation. Internal structure models generated by a Markov-Chain Monte Carlo process and consistent with the geodetic constraints possess a solid inner core with a radius (r ic ) between 0.3 and 0.7 that of the outer core (r oc ).

Solar system expansion and strong equivalence principle as seen by the NASA MESSENGER mission.

The NASA MESSENGER mission explored the innermost planet of the solar system and obtained a rich data set of range measurements for the determination of Mercury's ephemeris. Here we use these precise data collected over 7 years to estimate parameters related to general relativity and the evolution of the Sun. These results confirm the validity of the strong equivalence principle with a significantly refined uncertainty of the Nordtvedt parameter η = (-6.6 ± 7.2) × 10-5. By assuming a metric theory of gravitation, we retrieved the post-Newtonian parameter ß = 1 + (-1.6 ± 1.8) × 10-5 and the Sun's gravitational oblateness, [Formula: see text] = (2.246 ± 0.022) × 10-7. Finally, we obtain an estimate of the time variation of the Sun gravitational parameter, [Formula: see text] = (-6.13 ± 1.47) × 10-14, which is consistent with the expected solar mass loss due to the solar wind and interior processes. This measurement allows us to constrain [Formula: see text] to be <4 × 10-14 per year.

Orbit determination of the Lunar Reconnaissance Orbiter: Status after Seven Years.

The Lunar Reconnaissance Orbiter (LRO) has been orbiting the Moon since 2009, obtaining unique and foundational datasets important to understanding the evolution of the Moon and the Solar System. The high-resolution data acquired by LRO benefit from precise orbit determination (OD), limiting the need for geolocation and co-registration tasks. The initial position knowledge requirement (50 meters) was met with radio tracking from ground stations, after combination with LOLA altimetric crossovers. LRO-specific gravity field solutions were determined and allowed radio-only OD to perform at the level of 20 meters, although secular inclination changes required frequent updates. The high-accuracy gravity fields from GRAIL, with <10 km spatial resolution, further improved the radio-only orbit reconstruction quality (<10 meters). However, orbit reconstruction is in part limited by the 0.3-0.5 mm/s measurement noise level in S-band tracking. One-way tracking through Laser Ranging can supplement the tracking available for OD with 28-Hz ranges with 20-cm single-shot precision, but is available only on the nearside (the lunar hemisphere facing the Earth due to tidal locking). Here, we report on the status of the OD effort since the beginning of the mission, a period spanning more than seven years. We describe modeling improvements and the use of new measurements. In particular, the LOLA altimetric data give accurate, uniform, and independent information about LRO's orbit, with a different sensitivity and geometry which includes coverage over the lunar farside and is not tied to ground-based assets. With SLDEM2015 (a combination of the LOLA topographic profiles and the Kaguya Terrain Camera stereo images), another use of altimetry is possible for OD. We extend the 'direct altimetry' technique developed for the ICESat mission to perform OD and adjust spacecraft position to minimize discrepancies between LOLA tracks and SLDEM2015. Comparisons with the radio-only orbits are used to evaluate this new tracking type, of interest for the OD of future lunar orbiters carrying a laser altimeter. LROC NAC images also provide independent accuracy estimation, through the repeated views taken of anthropogenic features for instance.

Evidence for a Low Bulk Crustal Density for Mars from Gravity and Topography.

Knowledge of the average density of the crust of a planet is important in determining its interior structure. The combination of high-resolution gravity and topography data has yielded a low density for the Moon's crust, yet for other terrestrial planets the resolution of the gravity field models has hampered reasonable estimates. By using well-chosen constraints derived from topography during gravity field model determination using satellite tracking data, we show that we can robustly and independently determine the average bulk crustal density directly from the tracking data, using the admittance between topography and imperfect gravity. We find a low average bulk crustal density for Mars, 2582 ± 209 kg m-3. This bulk crustal density is lower than that assumed until now. Densities for volcanic complexes are higher, consistent with earlier estimates, implying large lateral variations in crustal density. In addition, we find indications that the crustal density increases with depth.

Gravity field of the Orientale basin from the Gravity Recovery and Interior Laboratory Mission.

The Orientale basin is the youngest and best-preserved major impact structure on the Moon. We used the Gravity Recovery and Interior Laboratory (GRAIL) spacecraft to investigate the gravitational field of Orientale at 3- to 5-kilometer (km) horizontal resolution. A volume of at least (3.4 ± 0.2) × 106 km3 of crustal material was removed and redistributed during basin formation. There is no preserved evidence of the transient crater that would reveal the basin's maximum volume, but its diameter may now be inferred to be between 320 and 460 km. The gravity field resolves distinctive structures of Orientale's three rings and suggests the presence of faults associated with the outer two that penetrate to the mantle. The crustal structure of Orientale provides constraints on the formation of multiring basins.

Lunar impact basins revealed by Gravity Recovery and Interior Laboratory measurements.

Observations from the Gravity Recovery and Interior Laboratory (GRAIL) mission indicate a marked change in the gravitational signature of lunar impact structures at the morphological transition, with increasing diameter, from complex craters to peak-ring basins. At crater diameters larger than ~200 km, a central positive Bouguer anomaly is seen within the innermost peak ring, and an annular negative Bouguer anomaly extends outward from this ring to the outer topographic rim crest. These observations demonstrate that basin-forming impacts remove crustal materials from within the peak ring and thicken the crust between the peak ring and the outer rim crest. A correlation between the diameter of the central Bouguer gravity high and the outer topographic ring diameter for well-preserved basins enables the identification and characterization of basins for which topographic signatures have been obscured by superposed cratering and volcanism. The GRAIL inventory of lunar basins improves upon earlier lists that differed in their totals by more than a factor of 2. The size-frequency distributions of basins on the nearside and farside hemispheres of the Moon differ substantially; the nearside hosts more basins larger than 350 km in diameter, whereas the farside has more smaller basins. Hemispherical differences in target properties, including temperature and porosity, are likely to have contributed to these different distributions. Better understanding of the factors that control basin size will help to constrain models of the original impactor population.

GRGM900C: A degree 900 lunar gravity model from GRAIL primary and extended mission data.

We have derived a gravity field solution in spherical harmonics to degree and order 900, GRGM900C, from the tracking data of the Gravity Recovery and Interior Laboratory (GRAIL) Primary (1 March to 29 May 2012) and Extended Missions (30 August to 14 December 2012). A power law constraint of 3.6 ×10-4/ℓ2 was applied only for degree ℓ greater than 600. The model produces global correlations of gravity, and gravity predicted from lunar topography of ≥ 0.98 through degree 638. The model's degree strength varies from a minimum of 575-675 over the central nearside and farside to 900 over the polar regions. The model fits the Extended Mission Ka-Band Range Rate data through 17 November 2012 at 0.13 µm/s RMS, whereas the last month of Ka-Band Range-Rate data obtained from altitudes of 2-10 km fit at 0.98 µm/s RMS, indicating that there is still signal inherent in the tracking data beyond degree 900.

High-resolution local gravity model of the south pole of the Moon from GRAIL extended mission data.

We estimated a high-resolution local gravity field model over the south pole of the Moon using data from the Gravity Recovery and Interior Laboratory's extended mission. Our solution consists of adjustments with respect to a global model expressed in spherical harmonics. The adjustments are expressed as gridded gravity anomalies with a resolution of 1/6° by 1/6° (equivalent to that of a degree and order 1080 model in spherical harmonics), covering a cap over the south pole with a radius of 40°. The gravity anomalies have been estimated from a short-arc analysis using only Ka-band range-rate (KBRR) data over the area of interest. We apply a neighbor-smoothing constraint to our solution. Our local model removes striping present in the global model; it reduces the misfit to the KBRR data and improves correlations with topography to higher degrees than current global models. KEY POINTS: We present a high-resolution gravity model of the south pole of the Moon Improved correlations with topography to higher degrees than global models Improved fits to the data and reduced striping that is present in global models.

Gravity field of the Moon from the Gravity Recovery and Interior Laboratory (GRAIL) mission.

Spacecraft-to-spacecraft tracking observations from the Gravity Recovery and Interior Laboratory (GRAIL) have been used to construct a gravitational field of the Moon to spherical harmonic degree and order 420. The GRAIL field reveals features not previously resolved, including tectonic structures, volcanic landforms, basin rings, crater central peaks, and numerous simple craters. From degrees 80 through 300, over 98% of the gravitational signature is associated with topography, a result that reflects the preservation of crater relief in highly fractured crust. The remaining 2% represents fine details of subsurface structure not previously resolved. GRAIL elucidates the role of impact bombardment in homogenizing the distribution of shallow density anomalies on terrestrial planetary bodies.

Gravity field and internal structure of Mercury from MESSENGER.

Radio tracking of the MESSENGER spacecraft has provided a model of Mercury's gravity field. In the northern hemisphere, several large gravity anomalies, including candidate mass concentrations (mascons), exceed 100 milli-Galileos (mgal). Mercury's northern hemisphere crust is thicker at low latitudes and thinner in the polar region and shows evidence for thinning beneath some impact basins. The low-degree gravity field, combined with planetary spin parameters, yields the moment of inertia C/MR(2) = 0.353 ± 0.017, where M and R are Mercury's mass and radius, and a ratio of the moment of inertia of Mercury's solid outer shell to that of the planet of C(m)/C = 0.452 ± 0.035. A model for Mercury's radial density distribution consistent with these results includes a solid silicate crust and mantle overlying a solid iron-sulfide layer and an iron-rich liquid outer core and perhaps a solid inner core.

Farside gravity field of the moon from four-way Doppler measurements of SELENE (Kaguya).

The farside gravity field of the Moon is improved from the tracking data of the Selenological and Engineering Explorer (SELENE) via a relay subsatellite. The new gravity field model reveals that the farside has negative anomaly rings unlike positive anomalies on the nearside. Several basins have large central gravity highs, likely due to super-isostatic, dynamic uplift of the mantle. Other basins with highs are associated with mare fill, implying basalt eruption facilitated by developed faults. Basin topography and mantle uplift on the farside are supported by a rigid lithosphere, whereas basins on the nearside deformed substantially with eruption. Variable styles of compensation on the near- and farsides suggest that reheating and weakening of the lithosphere on the nearside was more extensive than previously considered.