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The worldwide coronavirus disease 2019 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce 2 pH-sensitive “LAMPshade” dyes as novel readouts in an isothermal Reverse Transcriptase Loop-mediated isothermal AMPlification amplification assay for severe acute respiratory syndrome coronavirus 2 RNA. The resulting JaneliaLAMP assay is robust, simple, inexpensive, and has low technical requirements, and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

Femtosecond lasers at fixed wavelengths above 1,000 nm are powerful, stable and inexpensive, making them promising sources for two-photon microscopy. Biosensors optimized for these wavelengths are needed for both next-generation microscopes and affordable turn-key systems. Here we report jYCaMP1, a yellow variant of the calcium indicator jGCaMP7 that outperforms its parent in mice and flies at excitation wavelengths above 1,000 nm and enables improved two-color calcium imaging with red fluorescent protein-based indicators. jYCaMP1, a yellow variant of the calcium indicator jGCaMP7, enables fast multicolor two-photon imaging at excitation wavelengths above 1,000 nm for use with popular ytterbium-doped fiber and modelocked semiconductor lasers.

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems. The popular GCaMP indicators are based on the calcium-binding protein calmodulin and the RS20 peptide. These sensors report neural activity at timescales much slower than electrical signaling, limited by their biophysical properties and trade-offs between sensitivity and speed. We used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting ‘jGCaMP8’ sensors, based on calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (rise times, 2 ms) and still feature the highest sensitivity for neural activity reported for any protein-based sensor. jGCaMP8 sensors will allow tracking of larger populations of neurons on timescales relevant to neural computation.

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems. The popular GCaMP indicators are based on the calcium-binding protein calmodulin and the RS20 peptide. These sensors report neural activity at timescales much slower than electrical signaling, limited by their biophysical properties and trade-offs between sensitivity and speed. We used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting ‘jGCaMP8’ sensors, based on calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (rise times, 2 ms) and still feature the highest sensitivity for neural activity reported for any protein-based sensor. jGCaMP8 sensors will allow tracking of larger populations of neurons on timescales relevant to neural computation.

Observations of structure at sub-galactic scales are crucial for probing the properties of dark matter, which is the dominant source of gravity in the universe. It will become increasingly important for future surveys to distinguish between line-of-sight halos and subhalos to avoid wrong inferences on the nature of dark matter. We reanalyze a sub-galactic structure (in lens JVAS B1938+666) that has been previously found using the gravitational imaging technique in galaxy-galaxy lensing systems. This structure has been assumed to be a satellite in the halo of the main lens galaxy. We fit the redshift of the perturber of the system as a free parameter, using the multi-plane thin-lens approximation, and find that the redshift of the perturber is $z_\mathrm{int} = 1.42\substack{+0.10 \\ -0.15}$ (with a main lens redshift of $z=0.881$). Our analysis indicates that this structure is more massive than the previous result by an order of magnitude. This constitutes the first dark perturber shown to be a line-of-sight halo with a gravitational lensing method., Comment: 15 pages, 2 tables, 15 figures. Code available at: https://github.com/acagansengul/interlopers_with_lenstronomy, v2: Modifications to analysis pipeline included, v3: Matches MNRAS published version

Galaxy-galaxy strong gravitational lenses have become a popular probe of dark matter (DM) by providing a window into structure formation on the smallest scales. In particular, the convergence power spectrum of subhalos within lensing galaxies has been suggested as a promising observable to study DM. However, the distances involved in strong-lensing systems are vast, and we expect the relevant volume to contain line-of-sight (LOS) halos that are not associated with the main lens. We develop a formalism to calculate the effect of LOS halos as an effective convergence power spectrum. The multi-lens plane equation couples the angular deflections of consecutive lens planes, but by assuming that the perturbations due to the LOS halos are small, we show that they can be projected onto the main-lens plane as effective subhalos. We test our formalism by simulating lensing systems using the full multi-plane lens equation and find excellent agreement. We show how the relative contribution of LOS halos and subhalos depends on the source and lens redshift, as well as the assumed halo and subhalo mass functions. For a fiducial system with fraction of DM halo mass in substructure $f_{\rm sub}=0.4\%$ for subhalo masses $[10^5-10^8]\rm{M}_{\odot}$, the interloper contribution to the power spectrum is at least several times greater than that of subhalos for source redshifts $z_s\gtrsim0.5$. Furthermore, it is likely that for the SLACS and BELLS lenses the interloper contribution dominates: $f_{\rm sub}\gtrsim2\%$ ($4\%$) is needed for subhalos to dominate in SLACS (BELLS), which is higher than current upper bounds on $f_{\rm sub}$ for our mass range. Since the halo mass function is better understood from first principles, the dominance of interlopers in galaxy-galaxy lenses with high-quality imaging can be seen as a significant advantage when translating this observable into a constraint on DM., Comment: 24 pages, 8 figures, Matches accepted version, v3: Fixed a typo in Eq. C4 in the appendix. No changes in the derivations

The recent emergence of multidrug-resistant Acinetobacter baumannii strains and the non-efficacy of currently available antibiotics against such infections have led to an urgent need for the development of novel antibacterials. In an effort to address this problem, we have identified three novel inhibitors, namely, D5, D12 and D6 using in silico screening with a homology model of the outer membrane protein W2 (OmpW2) from A. baumannii, as the proposed new drug target. OmpW is an eight-stranded β-barrel protein involved in the transport of hydrophobic molecules across the outer membrane and maintenance of homeostasis under cellular stress. The antimicrobial activities of compounds D5, D12 and D6 were evaluated against a panel of clinical isolates of A. baumannii strains. These compounds inhibited the growth of the strains with minimum inhibitory concentration (MIC) ranges of 1-32μg/mL. Time-kill kinetic studies with the highly virulent and multidrug-resistant strain, A. baumannii 5075, indicated that D6 exhibited the highest bactericidal activity asa≥3log10 CFU/mL (99.9%) reduction in colony count from the initial inoculum was observed after 30min incubation. D5 and D12 reduced at least 1log10 CFU/mL (90%) of the initial inoculum after 24h. In conclusion, these three lead inhibitors have provided two distinct chemical scaffolds for further analog design and optimizations, using chemical synthesis, to develop more potent inhibitors of the pathogen.

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

The ROOT Mathematical and Statistical libraries have been recently improved both to increase their performance and to facilitate the modelling of parametric functions that can be used for performing maximum likelihood fits to data sets to estimate parameters and their uncertainties. First, we report on the new functionalities introduced in ROOT’s TFormula and TF1 classes to build these models in a convenient way for the users. We show how function objects, represented in ROOT by TF1 classes, can be used as probability density functions and how they can be combined together—via an addition operator—to perform extended likelihood fit of several normalized components. We also describe the new operators introduced to perform the convolution of two functions. Finally, we report on the improvements in the performance of the ROOT fitting algorithm, by using SIMD vectorization when evaluating the model function on large data sets and by exploiting multi-thread parallelization when computing the likelihood function.

Deliberate and natural outbreaks of infectious disease, the prevalence of antibiotic resistant strains, and the ease by which antibiotic resistant bacteria can be intentionally engineered all underscore the necessity of effective vaccines and continued development of novel antimicrobial/antiviral therapeutics. Isoprenes, a group of molecules fundamentally involved in a variety of crucial biological functions, are derived from either the mevalonic acid (MVA) or methylerythritol phosphate (MEP) pathway. While mammals utilize the MVA pathway, many bacteria utilize the MEP pathway, highlighting the latter as an attractive target for antibiotic development. In this report we describe the cloning and characterization of Francisella tularensis MEP cytidylyltransferase, a MEP pathway enzyme and potential target for antibiotic development. Size exclusion chromatography indicates the protein exists as a dimer in solution. Enzyme assays produced an apparentK(MEP)(M) = 178 μM, K(CTP)(M) = 73 μM , k(MEP)(cat) = 1(s-1), k(CTP)(cat) = 0.8( s-1), and a k(MEP)(cat)/ K(MEP)(M) = 3.4 x 10(5) M(-1) min(-1). The enzyme exhibits a strict preference for Mg(+2) as a divalent cation and CTP as the nucleotide. Titanium dioxide chromatography-tandem mass spectrometry identified Thr141 as a site of phosphorylation. T141D and T141E site-directed mutants are catalytically inactive, suggesting a mechanism for post-translational control of metabolic flux through the F. tularensis MEP pathway. Overall, our study suggests that MEP cytidylyltransferase is an excellent target for the development of novel antibiotics against F. tularensis.