Spatial Distribution of Mycobacterium tuberculosis mRNA and Secreted Antigens in Acid-Fast Negative Human Antemortem and Resected Tissue

BACKGROUND: The ability to detect evidence of Mycobacterium tuberculosis (Mtb) infection within human tissues is critical to the study of Mtb physiology, tropism, and spatial distribution within TB lesions. The capacity of the widely-used Ziehl-Neelsen (ZN) staining method for identifying Mtb acid-fast bacilli (AFB) in tissue is highly variable, which can limit detection of Mtb bacilli for research and diagnostic purposes. Here, we sought to circumvent these limitations via detection of Mtb mRNA and secreted antigens in human tuberculous tissue. METHODS: We adapted RNAscope, an RNA in situ hybridisation (RISH) technique, to detect Mtb mRNA in ante- and postmortem human TB tissues and developed a dual ZN/immunohistochemistry staining approach to identify AFB and bacilli producing antigen 85B (Ag85B). FINDINGS: We identified Mtb mRNA within intact and disintegrating bacilli as well as extrabacillary mRNA. Mtb mRNA was distributed zonally within necrotic and non-necrotic granulomas. We also found Mtb mRNA within, and adjacent to, necrotic granulomas in ZN-negative lung tissue and in Ag85B-positive bronchiolar epithelium. Intriguingly, we observed accumulation of Mtb mRNA and Ag85B in the cytoplasm of host cells. Notably, many AFB were negative for Ag85B staining. Mtb mRNA was observed in ZN-negative antemortem lymph node biopsies. INTERPRETATION: RNAscope and dual ZN/immunohistochemistry staining are well-suited for identifying subsets of intact Mtb and/or bacillary remnants in human tissue. RNAscope can identify Mtb mRNA in ZN-negative tissues from patients with TB and may have diagnostic potential in complex TB cases. FUNDING: Wellcome Leap Delta Tissue Program, Wellcome Strategic Core Award, the National Institutes of Health (NIH, USA), the Mary Heersink Institute for Global Health at UAB, the UAB Heersink School of Medicine

Kaon Zero-Point Fluctuations in Neutron Star Matter

We investigate the contribution of zero-point motion, arising from fluctuations in kaon modes, to the ground state properties of neutron star matter containing a Bose condensate of kaons. The zero-point energy is derived via the thermodynamic partition function, by integrating out fluctuations for an arbitrary value of the condensate field. It is shown that the vacuum counterterms of the chiral Lagrangian ensure the cancellation of divergences dependent on $\mu$, the charge chemical potential, which may be regarded as an external vector potential. The total grand potential, consisting of the tree-level potential, the zero-point contribution, and the counterterm potential, is extremized to yield a locally charge neutral, beta-equilibrated and minimum energy ground state. In some regions of parameter space we encounter the well-known problem of a complex effective potential. Where the potential is real and solutions can be obtained, the contributions from fluctuations are found to be small in comparison with tree-level contributions.Comment: 40 pages RevTeX, 3 epsf figure

Optical modeling of the Jefferson Laboratory IR demo FEL

The Thomas Jefferson National Accelerator Facility (Jefferson Lab) is in the process of building a 1 kW free-electron laser operates at 3 microns. The details of the accelerator driver are given in other papers in these proceedings. The optical cavity consists of a near-concentric resonator with transmissive outcoupling. Though several free-electron lasers have used similar designs, they have not had to confront the high average-power loading present in this laser. It is useful to know the limits of this type of optical cavity design. The optical system of the laser has been modeled using the commercial code GLAD{reg_sign} by using a Beer`s-law region to mimic the FEL interaction. The effects of mirror heating have been calculated and compared with analytical treatments. The magnitude of the distortion for several materials and wave-lengths has been estimated. The model developed here allows one to quickly determine whether the mirror substrates and coatings are adequate for operation at a given optical power level once the absorption of the coatings, substrate, and transmission are known. Results of calculations of the maximum power level expected using several different sets of mirrors will be presented. Measurements of the distortion in calcium fluoride from absorption of carbon dioxide laser light are planned to benchmark the simulations. Multimode simulations using the code ELIXER have been carried out to characterize the saturated optical mode quality. The results will be presented

A versatile all-optical parity-time signal processing device using a Bragg grating induced using positive and negative Kerr-nonlinearity

The properties of gratings with Kerr nonlinearity and PT symmetry are investigated in this paper. The impact of the gain and loss saturation on the response of the grating is analysed for different input intensities and gain/loss parameters. Potential applications of these gratings as switches, logic gates and amplifiers are also shown

Altered sphingolipid pathway in SARS-CoV-2 infected human lung tissue

IntroductionThe SARS-CoV-2 mediated COVID-19 pandemic has impacted millions worldwide. Hyper-inflammatory processes, including cytokine storm, contribute to long-standing tissue injury and damage in COVID-19. The metabolism of sphingolipids as regulators of cell survival, differentiation, and proliferation has been implicated in inflammatory signaling and cytokine responses. Sphingosine-kinase-1 (SK1) and ceramide-synthase-2 (CERS2) generate metabolites that regulate the anti- and pro-apoptotic processes, respectively. Alterations in SK1 and CERS2 expression may contribute to the inflammation and tissue damage during COVID-19. The central objective of this study is to evaluate structural changes in the lung post-SARS-CoV-2 infection and to investigate whether the sphingolipid rheostat is altered in response to SARS-CoV-2 infection.MethodsCentral and peripheral lung tissues from COVID-19+ or control autopsies and resected lung tissue from COVID-19 convalescents were subjected to histologic evaluation of airspace and collagen deposisiton, and immunohistochemical evaluation of SK1 and CERS2.ResultsHere, we report significant reduction in air space and increase in collagen deposition in lung autopsy tissues from patients who died from COVID-19 (COVID-19+) and COVID-19 convalescent individuals. SK1 expression increased in the lungs of COVID-19+ autopsies and COVID-19 convalescent lung tissue compared to controls and was mostly associated with Type II pneumocytes and alveolar macrophages. No significant difference in CERS2 expression was noted. SARS-CoV-2 infection upregulates SK1 and increases the ratio of SK1 to CERS2 expression in lung tissues of COVID-19 autopsies and COVID-19 convalescents.DiscussionThese data suggest an alteration in the sphingolipid rheostat in lung tissue during COVID-19, suggesting a potential contribution to the inflammation and tissue damage associated with viral infection

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Predicted thermochemistry and unimolecular kinetics of nitrous sulfide

Article on predicted thermochemistry and unimolecular kinetics of nitrous sulfide

Search for the lepton-flavor-violating decays Bs0→e±μ∓ and B0→e±μ∓

A search for the lepton-flavor-violating decays Bs0→e±μ∓ and B0→e±μ∓ is performed with a data sample, corresponding to an integrated luminosity of 1.0  fb-1 of pp collisions at √s=7  TeV, collected by the LHCb experiment. The observed number of Bs0→e±μ∓ and B0→e±μ∓ candidates is consistent with background expectations. Upper limits on the branching fractions of both decays are determined to be B(Bs0→e±μ∓)101  TeV/c2 and MLQ(B0→e±μ∓)>126  TeV/c2 at 95% C.L., and are a factor of 2 higher than the previous bounds

Electro-thermal modelling for plasmonic structures in the TLM Method

This paper presents a coupled electromagnetic-thermal model for modelling temperature evolution in nano-size plasmonic heat sources. Both electromagnetic and thermal models are based on the Transmission Line Modelling (TLM) method and are coupled through a nonlinear and dispersive plasma material model. The stability and accuracy of the coupled EM-thermal model is analysed in the context of a nano-tip plasmonic heat source example