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BackgroundPrimary amoebic meningoencephalitis (PAM) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes.MethodsIn this study, we sequenced a full draft assembly of the Balamuthia mandrillaris genome (44.2 Mb in size) from a rare survivor of PAM, and recovered the mitochondrial genome from six additional Balamuthia strains. We also used unbiased metagenomic next-generation sequencing (NGS) and SURPI bioinformatics analysis to diagnose an ultimately fatal case of Balamuthia mandrillaris encephalitis in a 15-year-old girl.Results and DiscussionComparative analysis of the mitochondrial genome and high-copy number genes from six additional Balamuthia mandrillaris strains demonstrated remarkable sequence variation, and the closest Balamuthia homologs corresponded to other amoebae, hydroids, algae, slime molds, and peat moss. Real-time NGS testing of hospital day 6 CSF and brain biopsy samples detected Balamuthia on the basis of high-quality hits to 16S and 18S ribosomal RNA sequences present in the National Center for Biotechnology Information (NCBI) nt reference database. The presumptive diagnosis of PAM by visualization of amoebae on brain biopsy histopathology and NGS analysis was subsequently confirmed at the US Centers for Disease Control and Prevention (CDC) using a Balamuthia-specific PCR assay. Retrospective analysis of a day 1 CSF sample revealed that more timely identification of Balamuthia by metagenomic NGS, potentially resulting in a better clinical outcome, would have required availability of the complete genome sequence.ConclusionsThese results underscore the diverse evolutionary origins of Balamuthia mandrillaris, provide new targets for diagnostic assay development, and will facilitate further investigations of the biology and pathogenesis of this eukaryotic pathogen. The failure to identify PAM from a day 1 sample without a fully sequenced Balamuthia genome in the database highlights the critical importance of whole-genome reference sequences for microbial detection by metagenomic NGS.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0235-2) contains supplementary material, which is available to authorized users.

The origins of reflected light changes associated with neuronal activity (optical signals) were investigated in rat somatosensory cortex with optical imaging, microspectrophotometry, and laser-Doppler flowmetry, and dynamic changes in local hemoglobin concentration and oxygenation were focused on. Functional activation was carried out by 2-second, 5-Hz electrical stimulation of the hind limb under chloralose anesthesia. These measurements were performed at the contralateral parietal cortex through a thinned skull. Regional cortical blood flow (rCBF) started to rise 1.5 seconds after the stimulus onset, peaked at 3.5 seconds (26.7% +/- 9.7% increase over baseline), and returned to near baseline by 10 seconds. Optical signal responses at 577, 586, and 805 nm showed a monophasic increase in absorbance coincident with the increase in rCBF; however, the signal responses at 605 and 760 nm were biphasic (an early increase and late decrease in absorbance) and microanatomically heterogeneous. The spectral changes of absorbance indicated that the concentrations of both total hemoglobin and oxyhemoglobin increased together with rCBF; deoxyhemoglobin, increased slightly but distinctly (P = 0.016 at 1.0 seconds, P = 0.00038 at 1.5 seconds) just before rCBF increases, then decreased. The authors conclude that activity-related optical signals are greatly associated with a moment-to-moment adjustment of rCBF and metabolism to neuronal activity.

All-solid-state lithium-ion batteries (LIBs) are one of the promising candidates to overcome some issues of conventional LIBs with liquid electrolytes. However, high interfacial resistance of Li-ion transfer at the electrode/solid electrolyte limits their performance. Thus, it is important to clarify interfacial phenomena in a nanometer scale. Here, we present a new method to dynamically observe the Li-ion distribution and Co-ion electronic states in a LiCoO cathode of the all-solid-state LIB during charge and discharge reactions using operando scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). By applying a hyperspectral image analysis of non-negative matrix factorization (NMF) to the STEM-EELS, we succeeded in clearly observing the quantitative Li-ion distribution in the operando condition. We found from the operando observation with NMF that the Li ions did not uniformly extract/insert during the charge/discharge reactions, and the activity of the electrochemical reaction depended on the Li-ion concentration in a pristine state. An electrochemically inactive region was formed about 10-20 nm near the LiCoO/LiO-AlO-TiO-PO-based solid electrolyte interfaces. The STEM-EELS, electron diffraction, and Raman spectroscopy experimentally showed that the inactive region was a mixture of LiCoO and CoO, leading to the higher interfacial resistance of the Li-ion transfer because CoO does not have pathways of Li-ion diffusion in its crystal.

Lithium-ion transport in cathodes, anodes, solid electrolytes, and through their interfaces plays a crucial role in the electrochemical performance of solid-state lithium-ion batteries. Direct visualization of the lithium-ion dynamics at the nanoscale provides valuable insight for understanding the fundamental ion behaviour in batteries. Here, we report the dynamic changes of lithium-ion movement in a solid-state battery under charge and discharge reactions by time-resolved operando electron energy-loss spectroscopy with scanning transmission electron microscopy. Applying image denoising and super-resolution via sparse coding drastically improves the temporal and spatial resolution of lithium imaging. Dynamic observation reveals that the lithium ions in the lithium cobaltite cathode are complicatedly extracted with diffusion through the lithium cobaltite domain boundaries during charging. Even in the open-circuit state, they move inside the cathode. Operando electron energy-loss spectroscopy with sparse coding is a promising combination to visualize the ion dynamics and clarify the fundamentals of solid-state electrochemistry.