Acoustic resolution photoacoustic Doppler velocimetry in blood-mimicking fluids

Photoacoustic Doppler velocimetry provides a major opportunity to overcome limitations of existing blood flow measuring methods. By enabling measurements with high spatial resolution several millimetres deep in tissue, it could probe microvascular blood flow abnormalities characteristic of many different diseases. Although previous work has demonstrated feasibility in solid phantoms, measurements in blood have proved significantly more challenging. This difficulty is commonly attributed to the requirement that the absorber spatial distribution is heterogeneous relative to the minimum detectable acoustic wavelength. By undertaking a rigorous study using blood-mimicking fluid suspensions of 3 μm absorbing microspheres, it was discovered that the perceived heterogeneity is not only limited by the intrinsic detector bandwidth; in addition, bandlimiting due to spatial averaging within the detector field-of-view also reduces perceived heterogeneity and compromises velocity measurement accuracy. These detrimental effects were found to be mitigated by high-pass filtering to select photoacoustic signal components associated with high heterogeneity. Measurement under-reading due to limited light penetration into the flow vessel was also observed. Accurate average velocity measurements were recovered using "range-gating", which furthermore maps the cross-sectional velocity profile. These insights may help pave the way to deep-tissue non-invasive mapping of microvascular blood flow using photoacoustic methods

Velocity measurements in whole blood using acoustic resolution photoacoustic Doppler

Acoustic resolution photoacoustic Doppler velocimetry promises to overcome the spatial resolution and depth penetration limitations of current blood flow measuring methods. Despite successful implementation using blood-mimicking fluids, measurements in blood have proved challenging, thus preventing in vivo application. A common explanation for this difficulty is that whole blood is insufficiently heterogeneous relative to detector frequencies of tens of MHz compatible with deep tissue photoacoustic measurements. Through rigorous experimental measurements we provide new insight that refutes this assertion. We show for the first time that, by careful choice of the detector frequency and field-of-view, and by employing novel signal processing methods, it is possible to make velocity measurements in whole blood using transducers with frequencies in the tens of MHz range. These findings have important implications for the prospects of making deep tissue measurements of blood flow relevant to the study of microcirculatory abnormalities associated with cancer, diabetes, atherosclerosis and other conditions

The Enigmatic (Almost) Dark Galaxy Coma P: Distance Measurement and Stellar Populations from HST Imaging

We present Hubble Space Telescope (HST) observations of the low surface brightness (SB) galaxy Coma P. This system was first discovered in the Arecibo Legacy Fast ALFA HI survey and was cataloged as an (almost) dark galaxy because it did not exhibit any obvious optical counterpart in the available survey data (e.g., Sloan Digital Sky Survey). Subsequent WIYN pODI imaging revealed an ultra-low SB stellar component located at the center of the HI detection. We use the HST images to produce a deep color-magnitude diagram (CMD) of the resolved stellar population present in Coma P. We clearly detect a red stellar sequence that we interpret to be a red giant branch, and use it to infer a tip of the red giant branch (TRGB) distance of 5.50$^{+0.28}_{-0.53}$ Mpc. The new distance is substantially lower than earlier estimates and shows that Coma P is an extreme dwarf galaxy. Our derived stellar mass is only 4.3 $\times$ 10$^5$ $M_\odot$, meaning that Coma P has an extreme HI-to-stellar mass ratio of 81. We present a detailed analysis of the galaxy environment within which Coma P resides. We hypothesize that Coma P formed within a local void and has spent most of its lifetime in a low-density environment. Over time, the gravitational attraction of the galaxies located in the void wall has moved it to the edge, where it had a recent "fly-by" interaction with M64. We investigate the possibility that Coma P is at a farther distance and conclude that the available data are best fit by a distance of 5.5 Mpc.Comment: 22 pages, 11 figures. Accepted for publication in the Astronomical Journa

Molecular mechanisms of drug resistance in natural Leishmania populations vary with genetic background

The evolution of drug-resistance in pathogens is a major global health threat. Elucidating the molecular basis of pathogen drug-resistance has been the focus of many studies but rarely is it known whether a drug-resistance mechanism identified is universal for the studied pathogen; it has seldom been clarified whether drug-resistance mechanisms vary with the pathogen's genotype. Nevertheless this is of critical importance in gaining an understanding of the complexity of this global threat and in underpinning epidemiological surveillance of pathogen drug resistance in the field. This study aimed to assess the molecular and phenotypic heterogeneity that emerges in natural parasite populations under drug treatment pressure. We studied lines of the protozoan parasite Leishmania (L.) donovani with differential susceptibility to antimonial drugs; the lines being derived from clinical isolates belonging to two distinct genetic populations that circulate in the leishmaniasis endemic region of Nepal. Parasite pathways known to be affected by antimonial drugs were characterised on five experimental levels in the lines of the two populations. Characterisation of DNA sequence, gene expression, protein expression and thiol levels revealed a number of molecular features that mark antimonial-resistant parasites in only one of the two populations studied. A final series of in vitro stress phenotyping experiments confirmed this heterogeneity amongst drug-resistant parasites from the two populations. These data provide evidence that the molecular changes associated with antimonial-resistance in natural Leishmania populations depend on the genetic background of the Leishmania population, which has resulted in a divergent set of resistance markers in the Leishmania populations. This heterogeneity of parasite adaptations provides severe challenges for the control of drug resistance in the field and the design of molecular surveillance tools for widespread applicability

Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other.ope

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface

OBJECTIVES: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. METHODS: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. RESULTS: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. CONCLUSIONS: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries

The Physical Conditions of Emission-Line Galaxies at Cosmic Dawn from JWST/NIRSpec Spectroscopy in the SMACS 0723 Early Release Observations

We present rest-frame optical emission-line flux ratio measurements for five $z>5$ galaxies observed by the JWST Near-Infared Spectrograph (NIRSpec) in the SMACS 0723 Early Release Observations. We add several quality-control and post-processing steps to the NIRSpec pipeline reduction products in order to ensure reliable relative flux calibration of emission lines that are closely separated in wavelength, despite the uncertain \textit{absolute} spectrophotometry of the current version of the reductions. Compared to $z\sim3$ galaxies in the literature, the $z>5$ galaxies have similar [OIII]$\lambda$5008/H$\beta$ ratios, similar [OIII]$\lambda$4364/H$\gamma$ ratios, and higher ($\sim$0.5 dex) [NeIII]$\lambda$3870/[OII]$\lambda$3728 ratios. We compare the observations to MAPPINGS V photoionization models and find that the measured [NeIII]$\lambda$3870/[OII]$\lambda$3728, [OIII]$\lambda$4364/H$\gamma$, and [OIII]$\lambda$5008/H$\beta$ emission-line ratios are consistent with an interstellar medium that has very high ionization ($\log(Q) \simeq 8-9$, units of cm~s$^{-1}$), low metallicity ($Z/Z_\odot \lesssim 0.2$), and very high pressure ($\log(P/k) \simeq 8-9$, units of cm$^{-3}$). The combination of [OIII]$\lambda$4364/H$\gamma$ and [OIII]$\lambda$(4960+5008)/H$\beta$ line ratios indicate very high electron temperatures of $4.1<\log(T_e/{\rm K})<4.4$, further implying metallicities of $Z/Z_\odot \lesssim 0.2$ with the application of low-redshift calibrations for ``$T_e$-based'' metallicities. These observations represent a tantalizing new view of the physical conditions of the interstellar medium in galaxies at cosmic dawn.Comment: Accepted for publication in AAS Journals. 14 pages, 6 figures, 3 table