Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

Background Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves the glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethanesulfonate) into acetaldehyde and sulfite. Results We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis. Conclusions We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut.

Bacterial Nanocompartments: Structures, Functions and Applications

Increasing efficiency is an important driving force behind cellular organization and often achieved through compartmentalization. Long recognized as a core principle of eukaryotic cell organization, its widespread occurrence in prokaryotes has only recently come to light. Despite the early discovery of a few microcompartments such as gas vesicles and carboxysomes, the vast majority of these structures in prokaryotes are less than 100 nm in diameter - too small for conventional light microscopy and electron microscopic thin sectioning. Consequently, these smaller-sized nanocompartments have therefore been discovered serendipitously and then through bioinformatics shown to be broadly distributed. Their small uniform size, robust self-assembly, high stability, excellent biocompatibility, and large cargo capacity make them excellent candidates for biotechnology applications. This review will highlight our current knowledge of nanocompartments, the prospects for applications as well as open question and challenges that need to be addressed to fully understand these important structures.

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

Background: Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2 aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves a glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslAB), which cleaves isethionate (2 hydroxyethane sulfonate) into acetaldehyde and sulfite. Results: We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis. Conclusions: We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut.

Controlling nanochannel orientation and dimensions in graphene-based nanofluidic membranes

There is great interest in exploiting van der Waals gaps in layered materials as nanofluidic channels. Graphene oxide (GO) nanosheets are known to spontaneously assemble into stacked planar membranes with transport properties that are highly selective to molecular structure. Use of conventional GO membranes in liquid-phase applications is often limited by low flux values, due to intersheet nanochannel alignment perpendicular to the desired Z-directional transport, which leads to circuitous fluid pathways that are orders of magnitude longer than the membrane thickness. Here we demonstrate an approach that uses compressive instability in Zr-doped GO thin films to create wrinkle patterns that rotate nanosheets to high angles. Capturing this structure in polymer matrices and thin sectioning produce fully dense membranes with arrays of near-vertically aligned nanochannels. These robust nanofluidic devices offer pronounced reduction in fluid path-length, while retaining the high selectivity for water over non-polar molecules characteristic of GO interlayer nanochannels.

New social insect nests from the Upper Jurassic Morrison Formation of Utah

This paper reports a new assemblage of social insect ichnofossils from the Brushy Basin Member of the Upper Jurassic Morrison Formation near Green River, Utah. At least seven distinct nests are visible in the locality horizon, identifiable at the outcrop scale by loci of anastomosing, and orthogonally connected hor-izontal burrows and vertical shafts. A boulder-sized block from the in situ horizon has eroded and rolled downhill, revealing the ventral aspect of the nest, showing a view of the overall nest architecture. Burrow and shaft clusters are organized into mega-galleries which have branching arms and ovate, bulbous cham-bers. The organization of distinct trace morphologies is consistent with ethological complexity of the social insects. A small sample was collected and analyzed by serial sectioning and petrographic thin sectioning to observe small-scale morphological features. Centimeter-scale analysis shows chamber, gallery, and burrow walls have complex topography. Pebble-sized, hollow, ellipsoid features are distributed throughout the up-permost facies of the nest and have undergone complete silicification of their outer surfaces. The ellipsoids share similarity with pellet structures made of mud or carton produced by modern termites. This trace fossil assemblage suggests it is possible that termites had acquired subterranean nesting behavior, and mud or carton utilization in nest construction in seasonally arid habitats by the Late Jurassic.

Observation of the Transport and Removal of Lipofuscin from the Mouse Myocardium using Transmission Electron Microscope

This study was performed to investigate whether the lipofuscin formed within cardiomyocytes can be excluded by the myocardial tissue. We have provided indicators that can be used for future studies on anti-aging interventions.In the present study, the heart of a 5-month-old BALB/c mouse was obtained for resin embedding and ultra-thin sectioning. The specimens were observed under a Hitach 7500 transmission electron microscope, and the images were acquired using an XR401 side-insertion device.Lipofuscin granules are found abundantly in myocardial cells. Cardiomyocytes can excrete lipofuscin granules into the myocardial interstitium using capsule-like protrusions that are formed on the sarcolemma. These granules enter the myocardial interstitium and can be de-aggregated to form “membrane-like garbage”, which can pass from the myocardial stroma into the lumen of the vessel through its walls in the form of soluble fine particles through diffusion or endocytosis of capillaries. Smaller lipofuscin granules can pass through the walls of the vessels and enter the blood vessel lumen through the active transport function of the capillary endothelial cells. When the extended cytoplasmic end of macrophages and fibroblasts fuse with the endothelial cells, the lipofuscin granules or clumps found in the cells of the myocardial interstitium are transported to the capillary walls, and then, they are released into the lumen of the blood vessel by the endothelial cells.The myocardial tissues of mice have the ability to eliminate the lipofuscin produced in the cardiomyocytes into the myocardial blood circulation. Although there are several mechanisms through which the myocardial tissues release lipofuscin into the bloodstream, it is mainly carried out in the form of small, fine, soluble, continuous transport.

Bryozoan fauna from the Mississippian of the Akuyuk section, southern Kazakhstan

Five bryozoan species are described from the lower part of the Akuyuk section (Late Viséan, Mississippian) in southern Kazakhstan. Thin sectioning and micro-computed tomography have been utilized to study this material in detail. These integrated and complex techniques have a high potential to reveal much detail, although recrystallization and weathering of colonies preclude in depth assessment of all microstructures in detail. The bryozoan assemblage is represented by reticulate (60%), ramose (20%) and pinnate (20%) growth habits. The bryozoan fauna, together with accompanying fossils, and microfacies are characteristic for an environment with a stable substrate subjected to moderate wave energy conditions.

The Cahokia Connection at the Lake Providence Mounds, Louisiana

Several hundred potentially exotic sherds were recovered from late Coles Creek period (ca. A.D. 1150 to 1260) contexts at the Lake Providence Mounds in northeast Louisiana. A number of these sherds appeared to represent the remains of vessels from Cahokia or sites in the American Bottom region of southern Illinois, while others likely were local copies of Cahokia vessels. A selected sample of these “exotic” sherds, along with recognized local specimens, were subjected to petrographic thin sectioning (petrographic analysis) and instrumental neutron activation analysis (INAA). These analyses suggested that some of the potentially exotic sherds were, indeed, from the American Bottom area, while others could not be sources to a specific region. Possible reasons for the exotic vessels at Lake Providence are discussed.

Detection of Graphene Materials in Fibers

A method for the identification of graphene materials in fibers by high-resolution transmission electron microscopy (HRTEM)-Energy Dispersive Spectroscopy (EDS) has been reported. Two ways to prepare samples are available, namely the dissolution extraction and the ultra-thin sectioning method. For samples prepared by any method, the graphene material in the fiber can be detected by the following steps. Firstly,the elemental composition of the microparticle is demonstrated by EDS. Secondly, the morphology of the particles in the fiber can be obtained by TEM, and the number of layers of graphene materials is able to observed directly from the edge of sheet.