SQ109, a 1,2-diamine related to ethambutol, is currently in clinical trials for the treatment of tuberculosis, but its mode of action remains unclear. Here, we demonstrate that SQ109 disrupts cell ...wall assembly, as evidenced by macromolecular incorporation assays and ultrastructural analyses. SQ109 interferes with the assembly of mycolic acids into the cell wall core of Mycobacterium tuberculosis, as bacilli exposed to SQ109 show immediate inhibition of trehalose dimycolate (TDM) production and fail to attach mycolates to the cell wall arabinogalactan. These effects were not due to inhibition of mycolate synthesis, since total mycolate levels were unaffected, but instead resulted in the accumulation of trehalose monomycolate (TMM), the precursor of TDM and cell wall mycolates. In vitro assays using purified enzymes showed that this was not due to inhibition of the secreted Ag85 mycolyltransferases. We were unable to achieve spontaneous generation of SQ109-resistant mutants; however, analogs of this compound that resulted in similar shutdown of TDM synthesis with concomitant TMM accumulation were used to spontaneously generate resistant mutants that were also cross-resistant to SQ109. Whole-genome sequencing of these mutants showed that these all had mutations in the essential mmpL3 gene, which encodes a transmembrane transporter. Our results suggest that MmpL3 is the target of SQ109 and that MmpL3 is a transporter of mycobacterial TMM.
Abstract
Motivation
Clustering patient omic data is integral to developing precision medicine because it allows the identification of disease subtypes. A current major challenge is the integration ...multi-omic data to identify a shared structure and reduce noise. Cluster analysis is also increasingly applied on single-omic data, for example, in single cell RNA-seq analysis for clustering the transcriptomes of individual cells. This technology has clinical implications. Our motivation was therefore to develop a flexible and effective spectral clustering tool for both single and multi-omic data.
Results
We present Spectrum, a new spectral clustering method for complex omic data. Spectrum uses a self-tuning density-aware kernel we developed that enhances the similarity between points that share common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to reduce noise and reveal underlying structures. Spectrum contains a new method for finding the optimal number of clusters (K) involving eigenvector distribution analysis. Spectrum can automatically find K for both Gaussian and non-Gaussian structures. We demonstrate across 21 real expression datasets that Spectrum gives improved runtimes and better clustering results relative to other methods.
Availability and implementation
Spectrum is available as an R software package from CRAN https://cran.r-project.org/web/packages/Spectrum/index.html.
Supplementary information
Supplementary data are available at Bioinformatics online.
Due to their higher planet–star mass ratios, M dwarfs are the easiest targets for detection of low-mass planets orbiting nearby stars using Doppler spectroscopy. Furthermore, because of their low ...masses and luminosities, Doppler measurements enable the detection of low-mass planets in their habitable zones that correspond to closer orbits than for solar-type stars. We re-analyse literature Ultraviolet and Visual Echelle Spectrograph (UVES) radial velocities of 41 nearby M dwarfs in a combination with new velocities obtained from publicly available spectra from the HARPS-ESO spectrograph of these stars in an attempt to constrain any low-amplitude Keplerian signals. We apply Bayesian signal detection criteria, together with posterior sampling techniques, in combination with noise models that take into account correlations in the data and obtain estimates for the number of planet candidates in the sample. More generally, we use the estimated detection probability function to calculate the occurrence rate of low-mass planets around nearby M dwarfs. We report eight new planet candidates in the sample (orbiting GJ 27.1, GJ 160.2, GJ 180, GJ 229, GJ 422, and GJ 682), including two new multiplanet systems, and confirm two previously known candidates in the GJ 433 system based on detections of Keplerian signals in the combined UVES and High Accuracy Radial velocity Planet Searcher (HARPS) radial velocity data that cannot be explained by periodic and/or quasi-periodic phenomena related to stellar activities. Finally, we use the estimated detection probability function to calculate the occurrence rate of low-mass planets around nearby M dwarfs. According to our results, M dwarfs are hosts to an abundance of low-mass planets and the occurrence rate of planets less massive than 10 M⊕ is of the order of one planet per star, possibly even greater. Our results also indicate that planets with masses between 3 and 10 M⊕ are common in the stellar habitable zones of M dwarfs with an estimated occurrence rate of 0.21
$^{+0.03}_{-0.05}$
planets per star.
At the start of the 2019-2020 influenza season, concern arose that circulating B/Victoria viruses of the globally emerging clade V1A.3 were antigenically drifted from the strain included in the ...vaccine. Intense B/Victoria activity was followed by circulation of genetically diverse A(H1N1)pdm09 viruses that were also antigenically drifted. We measured vaccine effectiveness (VE) in the United States against illness from these emerging viruses.
We enrolled outpatients aged ≥6 months with acute respiratory illness at 5 sites. Respiratory specimens were tested for influenza by reverse-transcriptase polymerase chain reaction (RT-PCR). Using the test-negative design, we determined influenza VE by virus subtype/lineage and genetic subclades by comparing odds of vaccination in influenza cases versus test-negative controls.
Among 8845 enrollees, 2722 (31%) tested positive for influenza, including 1209 (44%) for B/Victoria and 1405 (51%) for A(H1N1)pdm09. Effectiveness against any influenza illness was 39% (95% confidence interval CI: 32-44), 45% (95% CI: 37-52) against B/Victoria and 30% (95% CI: 21-39) against A(H1N1)pdm09-associated illness. Vaccination offered no protection against A(H1N1)pdm09 viruses with antigenically drifted clade 6B.1A 183P-5A+156K HA genes (VE 7%; 95% CI: -14 to 23%) which predominated after January.
Vaccination provided protection against influenza illness, mainly due to infections from B/Victoria viruses. Vaccine protection against illness from A(H1N1)pdm09 was lower than historically observed effectiveness of 40%-60%, due to late-season vaccine mismatch following emergence of antigenically drifted viruses. The effect of drift on vaccine protection is not easy to predict and, even in drifted years, significant protection can be observed.
Climate change in the past has led to significant changes in species' distributions. However, how individual species respond to climate change depends largely on their adaptations and environmental ...tolerances. In the Quaternary, temperate-adapted taxa are in general confined to refugia during glacials while cold-adapted taxa are in refugia during interglacials. In the Northern Hemisphere, evidence appears to be mounting that in addition to traditional southern refugia for temperate species, cryptic refugia existed in the North during glacials. Equivalent cryptic southern refugia, to the south of the more conventional high-latitude polar refugia, exist in montane areas during periods of warm climate, such as the current interglacial. There is also a continental/oceanic longitudinal gradient, which should be included in a more complete consideration of the interaction between species ranges and climates. Overall, it seems clear that there is large variation in both the size of refugia and the duration during which species are confined to them. This has implications for the role of refugia in the evolution of species and their genetic diversity.
The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive ...diagnostic applications, there is a need for detection technologies that can scale to test many samples
while simultaneously testing for many pathogens
. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents
self-organize in a microwell array
to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health
.
The purpose of this study was to expand our previously published sweat normative data/analysis (n = 506) to establish sport-specific normative data for whole-body sweating rate (WBSR), sweat Na
+
, ...and rate of sweat Na
+
loss (RSSL). Data from 1303 athletes were compiled from observational testing (2000-2017) using a standardized absorbent sweat patch technique to determine local sweat Na
+
and normalized to whole-body sweat Na
+
. WBSR was determined from change in exercise body mass, corrected for food/fluid intake and urine/stool loss. RSSL was the product of sweat Na
+
and WBSR. There were significant differences between sports for WBSR, with highest losses in American football (1.51 ± 0.70 L/h), then endurance (1.28 ± 0.57 L/h), followed by basketball (0.95 ± 0.42 L/h), soccer (0.94 ± 0.38 L/h) and baseball (0.83 ± 0.34 L/h). For RSSL, American football (55.9 ± 36.8 mmol/h) and endurance (51.7 ± 27.8 mmol/h) were greater than soccer (34.6 ± 19.2 mmol/h), basketball (34.5 ± 21.2 mmol/h), and baseball (27.2 ± 14.7 mmol/h). After ANCOVA, significant between-sport differences in adjusted means for WBSR and RSSL remained. In summary, due to the significant sport-specific variation in WBSR and RSSL, American football and endurance have the greatest need for deliberate hydration strategies.
Abbreviations: WBSR: whole body sweating rate; SR: sweating rate; Na
+
: sodium; RSSL: rate of sweat sodium loss
This study determined the relations between regional (REG) and whole body (WB) sweating rate (RSR and WBSR, respectively) as well as REG and WB sweat Na
+
concentration (Na
+
) during exercise. ...Twenty-six recreational athletes (17 men, 9 women) cycled for 90 min while WB sweat Na
+
was measured using the washdown technique. RSR and REG sweat Na
+
were measured from nine regions using absorbent patches. RSR and REG sweat Na
+
from all regions were significantly ( P < 0.05) correlated with WBSR ( r = 0.58–0.83) and WB sweat Na
+
( r = 0.74–0.88), respectively. However, the slope and y-intercept of the regression lines for most models were significantly different than 1 and 0, respectively. The coefficients of determination ( r
2
) were 0.44–0.69 for RSR predicting WBSR best predictors: dorsal forearm ( r
2
= 0.62) and triceps ( r
2
= 0.69) and 0.55–0.77 for REG predicting WB sweat Na
+
best predictors: ventral forearm ( r
2
= 0.73) and thigh ( r
2
= 0.77). There was a significant ( P < 0.05) effect of day-to-day variability on the regression model predicting WBSR from RSR at most regions but no effect on predictions of WB sweat Na
+
from REG. Results suggest that REG cannot be used as a direct surrogate for WB sweating responses. Nonetheless, the use of regression equations to predict WB sweat Na
+
from REG can provide an estimation of WB sweat Na
+
with an acceptable level of accuracy, especially using the forearm or thigh. However, the best practice for measuring WBSR remains conventional WB mass balance calculations since prediction of WBSR from RSR using absorbent patches does not meet the accuracy or reliability required to inform fluid intake recommendations.
NEW & NOTEWORTHY This study developed a body map of regional sweating rate and regional (REG) sweat electrolyte concentrations and determined the effect of within-subject (bilateral and day-to-day) and between-subject (sex) factors on the relations between REG and the whole body (WB). Regression equations can be used to predict WB sweat Na
+
concentration from REG, especially using the forearm or thigh. However, prediction of WB sweating rate from REG sweating rate using absorbent patches does not reach the accuracy or reliability required to inform fluid intake recommendations.
For the first time, a coding complete genome of an RNA virus has been sequenced in its original form. Previously, RNA was sequenced by the chemical degradation of radiolabeled RNA, a difficult method ...that produced only short sequences. Instead, RNA has usually been sequenced indirectly by copying it into cDNA, which is often amplified to dsDNA by PCR and subsequently analyzed using a variety of DNA sequencing methods. We designed an adapter to short highly conserved termini of the influenza A virus genome to target the (-) sense RNA into a protein nanopore on the Oxford Nanopore MinION sequencing platform. Utilizing this method with total RNA extracted from the allantoic fluid of influenza rA/Puerto Rico/8/1934 (H1N1) virus infected chicken eggs (EID
6.8 × 10
), we demonstrate successful sequencing of the coding complete influenza A virus genome with 100% nucleotide coverage, 99% consensus identity, and 99% of reads mapped to influenza A virus. By utilizing the same methodology one can redesign the adapter in order to expand the targets to include viral mRNA and (+) sense cRNA, which are essential to the viral life cycle, or other pathogens. This approach also has the potential to identify and quantify splice variants and base modifications, which are not practically measurable with current methods.
Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization ...breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env’s silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448gp120 glycan. Effective bNAbs can therefore be raised against HIV-1 Env’s silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.
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•Silentface (SF) bNAbs can reach substantial neutralization breadth and potency•Defined structure of a SF bNAb bound to an Env trimer•Binding of SF bNAb resulted in trimer asymmetry in the V3 region•SF antibodies have in vivo activity and potential for clinical use
VRC-PG05 was the only donor-derived antibody against the silentface (SF) of HIV-1 envelope described to date. Schoofs et al. identify the antibody SF12 and its relatives, which recognize the center of the SF with a different angle and more extensive protein recognition than VRC-PG05, thereby achieving substantial neutralizing ability and potential for clinical use.
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