Reductive Pentose Cycle and Formate Assimilation in Rhodopseudomonas palustris

Rhodopseudomonas palustris assimilated formate autotrophically as carbon dioxide and hydrogen arising from the activity of the formic hydrogenlyase system. Kinetic analyses of cell suspensions pulse-labeled with (14)C-formate or (14)C-bicarbonate showed similar distributions of incorporated radioactivity. In both cases phosphate esters were the first assimilation products. Ribulose diphosphate carboxylase, phosphoribose isomerase, and phosphoribulokinase, characteristic enzymes of the reductive pentose cycle, were present in extracts of cells grown on formate.     

Contribution of sea ice microbial production to Antarctic benthic communities is driven by sea ice dynamics and composition of functional guilds

Organic matter produced by the sea ice microbial community (SIMCo) is an important link between sea ice dynamics and secondary production in near‐shore food webs of Antarctica. Sea ice conditions in McMurdo Sound were quantified from time series of MODIS satellite images for Sept. 1 through Feb. 28 of 2007–2015. A predictable sea ice persistence gradient along the length of the Sound and evidence for a distinct change in sea ice dynamics in 2011 were observed. We used stable isotope analysis (δ¹³C and δ¹⁵N) of SIMCo, suspended particulate organic matter (SPOM) and shallow water (10–20 m) macroinvertebrates to reveal patterns in trophic structure of, and incorporation of organic matter from SIMCo into, benthic communities at eight sites distributed along the sea ice persistence gradient. Mass‐balance analysis revealed distinct trophic architecture among communities and large fluxes of SIMCo into the near‐shore food web, with the estimates ranging from 2 to 84% of organic matter derived from SIMCo for individual species. Analysis of patterns in density, and biomass of macroinvertebrate communities among sites allowed us to model net incorporation of organic matter from SIMCo, in terms of biomass per unit area (g/m²), into benthic communities. Here, organic matter derived from SIMCo supported 39 to 71 per cent of total biomass. Furthermore, for six species, we observed declines in contribution of SIMCo between years with persistent sea ice (2008–2009) and years with extensive sea ice breakout (2012–2015). Our data demonstrate the vital role of SIMCo in ecosystem function in Antarctica and strong linkages between sea ice dynamics and near‐shore secondary productivity. These results have important implications for our understanding of how benthic communities will respond to changes in sea ice dynamics associated with climate change and highlight the important role of shallow water macroinvertebrate communities as sentinels of change for the Antarctic marine ecosystem.     

Rotational and translational movement features of the pelvis and thorax during adult human locomotion

The kinematics of the pelvis and thorax are important in gait studies since their movement patterns are closely related to gait efficiency and 'smoothness' of locomotion. The purpose of this study was to identify features of normal gait patterns for later comparisons with pathological and developmental gait patterns. A two camera SELSPOT system interfaced with an HP1000 minicomputer was used to obtain three-dimensional kinematic/temporal data for the pelvis and thorax. Data from treadmill walking of eight adults were used for within subject (at different speeds) analyses. The analyses revealed a very complex pattern with a set of breakpoints which was consistent over all subjects. Some features were invariant over a range of walking speeds although the total range of motion changed considerably.     

Monoclonal antibodies against the ruminal bacterium Selenomonas ruminantium.

Monoclonal antibodies were raised against whole cells of two different strains of Selenomonas ruminantium and tested for specificity and sensitivity in immunofluorescence and enzyme-linked immunosorbent assay procedures. Species-specific and strain-specific antibodies were identified, and reactive antigens were demonstrated in solubilized cell wall extracts of S. ruminantium. A monoclonal antibody-based solid-phase immunoassay was established to quantify S. ruminantium in cultures or samples from the rumen, and this had a sensitivity of 0.01 to 0.02% from 10(7) cells. For at least one strain, the extent of antibody reaction varied depending upon the stage of bacterial growth. Antigen characterization by immunoblotting shows that monoclonal antibodies raised against two different strains of S. ruminantium reacted with the same antigen on each strain. For one strain, an additional antigen reacted with both monoclonal antibodies. In the appropriate assay, these monoclonal antibodies may have advantages over gene probes, both in speed and sensitivity, for bacterial quantification studies.     

Two-dimensional display and whole genome comparison of bacterial pathogen genomes of high G+C DNA content

Three highly mutable loci of the wall-less pathogens Mycoplasma bovis, Mycoplasma pulmonis and Mycoplasma agalactiae undergo high-frequency genomic rearrangements and generate extensive antigenic variation of major surface lipoproteins. Adjacent to each locus, an open reading frame exists as a single chromosomal copy and is predicted to encode a site-specific DNA recombinase exhibiting high homology to the recombinases XerD of Escherichia coli and CodV of Bacillus subtilis. Each of the mycoplasmal proteins are members of the lambda integrase family of tyrosine site-specific recombinases and likely mediates site-specific DNA inversions observed within the adjacent, variable loci.     

Do diversity of plants,soil fungi and bacteria influence aggregate stability on ultramafic Ferralsols? A metagenomic approach in a tropical hotspot of biodiversity

Plant and Soil - Understanding how soil aggregate stability (MWD) is influenced by microbial diversity and abundance can be crucial for ecological restoration in severely disturbed areas. We...     

Biomechanical modeling of posterior instrumentation of the scoliotic spine

Scoliosis is a three-dimensional deformation of the spine that can be treated by vertebral fusion using surgical instrumentation. However, the optimal configuration of instrumentation remains controversial. Simulating the surgical maneuvers with personalized biomechanical models may provide an analytical tool to determine instrumentation configuration during the pre-operative planning. Finite element models used in surgical simulations display convergence difficulties as a result of discontinuities and stiffness differences between elements. A kinetic model using flexible mechanisms has been developed to address this problem, and this study presents its use in the simulation of Cotrel-Dubousset Horizon surgical maneuvers. The model of the spine is composed of rigid bodies corresponding to the thoracic and lumbar vertebrae, and flexible elements representing the intervertebral structures. The model was personalized to the geometry of three scoliotic patients (with a thoracic Cobb angle of 45 degrees, 49 degrees and 39 degrees ). Binary joints and kinematic constraints were used to represent the rod-implant-vertebra joints. The correction procedure was simulated using three steps: (1) Translation of hooks and screws on the first rod; (2) 90 degrees rod rotation; (3) Hooks and screws look-up on the rod. After the simulation, slight differences of 0-6 degrees were found for the thoracic spine scoliosis and the kyphosis, and of 1-8 degrees for the axial rotation of the apical vertebra and for the orientation of the plane of maximum deformity, compared to the real post-operative shape of the patient. Reaction loads at the vertebra-implant link were mostly below 1000 N, while reaction loads at the boundary conditions (representing the overall action of the surgeon) were in the range 7-470 N and maximum torque applied to the rod was 1.8 Nm. This kinetic modeling approach using flexible mechanisms provided a realistic representation of the surgical maneuvers. It may offer a tool to predict spinal geometry correction and assist in the pre-operative planning of surgical instrumentation of the scoliotic spine.     

Integrated gut/liver microphysiological systems elucidates inflammatory inter‐tissue crosstalk

A capability for analyzing complex cellular communication among tissues is important in drug discovery and development, and in vitro technologies for doing so are required for human applications. A prominent instance is communication between the gut and the liver, whereby perturbations of one tissue can influence behavior of the other. Here, we present a study on human gut‐liver tissue interactions under normal and inflammatory contexts, via an integrative multi‐organ platform comprising human liver (hepatocytes and Kupffer cells), and intestinal (enterocytes, goblet cells, and dendritic cells) models. Our results demonstrated long‐term (>2 weeks) maintenance of intestinal (e.g., barrier integrity) and hepatic (e.g., albumin) functions in baseline interaction. Gene expression data comparing liver in interaction with gut, versus isolation, revealed modulation of bile acid metabolism. Intestinal FGF19 secretion and associated inhibition of hepatic CYP7A1 expression provided evidence of physiologically relevant gut‐liver crosstalk. Moreover, significant non‐linear modulation of cytokine responses was observed under inflammatory gut‐liver interaction; for example, production of CXCR3 ligands (CXCL9,10,11) was synergistically enhanced. RNA‐seq analysis revealed significant upregulation of IFNα/β/γ signaling during inflammatory gut‐liver crosstalk, with these pathways implicated in the synergistic CXCR3 chemokine production. Exacerbated inflammatory response in gut‐liver interaction also negatively affected tissue‐specific functions (e.g., liver metabolism). These findings illustrate how an integrated multi‐tissue platform can generate insights useful for understanding complex pathophysiological processes such as inflammatory organ crosstalk. Biotechnol. Bioeng. 2017;114: 2648–2659. © 2017 Wiley Periodicals, Inc.     

A structural model for the catalytic cycle of Ca(2+)-ATPase

Ca(2+)-ATPase is responsible for active transport of calcium ions across the sarcoplasmic reticulum membrane. This coupling involves an ordered sequence of reversible reactions occurring alternately at the ATP site within the cytoplasmic domains, or at the calcium transport sites within the transmembrane domain. These two sites are separated by a large distance and conformational changes have long been postulated to play an important role in their coordination. To characterize the nature of these conformational changes, we have built atomic models for two reaction intermediates and postulated the mechanisms governing the large structural changes. One model is based on fitting the X-ray crystallographic structure of Ca(2+)-ATPase in the E1 state to a new 6 A structure by cryoelectron microscopy in the E2 state. This fit indicates that calcium binding induces enormous movements of all three cytoplasmic domains as well as significant changes in several transmembrane helices. We found that fluorescein isothiocyanate displaced a decavanadate molecule normally located at the intersection of the three cytoplasmic domains, but did not affect their juxtaposition; this result indicates that our model likely reflects a native E2 conformation and not an artifact of decavanadate binding. To explain the dramatic structural effect of calcium binding, we propose that M4 and M5 transmembrane helices are responsive to calcium binding and directly induce rotation of the phosphorylation domain. Furthermore, we hypothesize that both the nucleotide-binding and beta-sheet domains are highly mobile and driven by Brownian motion to elicit phosphoenzyme formation and calcium transport, respectively. If so, the reaction cycle of Ca(2+)-ATPase would have elements of a Brownian ratchet, where the chemical reactions of ATP hydrolysis are used to direct the random thermal oscillations of an innately flexible molecule.     

First Direct Evidence of Chalcolithic Footwear from the Near Eastern Highlands

In 2008, a well preserved and complete shoe was recovered at the base of a Chalcolithic pit in the cave of Areni-1, Armenia. Here, we discuss the chronology of this find, its archaeological context and its relevance to the study of the evolution of footwear. Two leather samples and one grass sample from the shoe were dated at the Oxford Radiocarbon Accelerator Unit (ORAU). A third leather sample was dated at the University of California-Irvine Accelerator Mass Spectrometry Facility (UCIAMS). The R_Combine function for the three leather samples provides a date range of 3627–3377 Cal BC (95.4% confidence interval) and the calibrated range for the straw is contemporaneous (3627–3377 Cal BC). The shoe was stuffed with loose, unfastened grass (Poaceae) without clear orientation which was more than likely used to maintain the shape of the shoe and/or prepare it for storage. The shoe is 24.5 cm long (European size 37), 7.6 to 10 cm wide, and was made from a single piece of leather that wrapped around the foot. It was worn and shaped to the wearer''s right foot, particularly around the heel and hallux where the highest pressure is exerted in normal gait. The Chalcolithic shoe provides solid evidence for the use of footwear among Old World populations at least since the Chalcolithic. Other 4^th millennium discoveries of shoes (Italian and Swiss Alps), and sandals (Southern Israel) indicate that more than one type of footwear existed during the 4^th millennium BC, and that we should expect to discover more regional variations in the manufacturing and style of shoes where preservation conditions permit.