Autonomous adaptive data acquisition for scanning hyperspectral imaging

Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively

Estimation of the Cellular Antioxidant Response to Chromium Action Using ESR Method

In the present study, the antioxidant capacity of chromium-treated L-41 (human epithelial-like cells) was investigated by the ESR spin-trapping technique. The crude cell extracts of the cells grown in the presence of 2 µM (nontoxic) and 20 µM (toxic) chromium (VI) concentrations were tested in the model Fenton system with and without catalase-inhibitor sodium azide. The presented approach using the ESR technique along with inhibitors lets us discern cell extract defense capacity connected with the enzymatic activity in viable cells and the catabolic activity in dying cells

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria.

Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community

A Calorimetric Characterization of Cr(VI)-Reducing Arthrobacter oxydans

This is the first of a series of calorimetric studies designed to characterize and understand survival mechanisms of metal-reducing bacteria isolated from metal-polluted environments. In this paper we introduce a new concept of thermal spectrum of the endothermic melting of complex biological systems (e.g., proteins, nucleic acids, ribosomes, membrane structures) in intact cells. All thermal spectra measured are thermograms that describe the temperature dependence of heat capacity change of the complex systems of biologically active substances in bacterial cells. This new concept of thermal spectrum was applied to investigate spectral features from intact cells of Cr(VI)-reducer Arthrobacter oxydans at different points of their growth conditions and stages. Over the temperature range of 40–105°C, we observed that spectral changes are particularly significant in the 40–90°C interval. This may correspond to the orderly changes in subcellular structural elements: proteins, ribosomes and RNA, membranes, and various structural elements of the cell wall during different points of the growth cycle and growth conditions. Spectral changes in the 90–105°C region are less pronounced, implicating that the structural composition of DNA-Protein (DNP) complexes may change little

Real-Time Molecular Monitoring of Chemical Environment in Obligate Anaerobes during Oxygen Adaptive Response

Determining the transient chemical properties of the intracellular environment can elucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms which enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier Transform Infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bonding in their cellular water. We observed a sequence of well orchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. This ability to monitor chemical changes at the molecular level can yield important insights into a wide range of adaptive responses

Synchrotron radiation infrared spectromicroscopy: a non-invasive molecular probe for biogeochemical processes

A long-standing desire in biogeochemistry is to be able to examine the cycling of elements by microorganisms as the processes are happening on surfaces of earth and environmental materials. Over the past decade, physics, engineering and instrumentation innovations have led to the introduction of synchrotron radiation-based infrared spectromicroscopy. Spatial resolutions of less than ten micrometers and photon energies of less than an electron volt make synchrotron infrared spectromicroscopy non-invasive and useful for following the course of biogeochemical processes on complex heterogeneous surfaces of earth and environmental materials. In this review, we will firstbriefly describe the technology, and then present several examples demonstrating its application potentials of the technology in probing and imaging biogeochemical processes