Identification of the Major Expressed S-Layer and Cell Surface-Layer-Related Proteins in the Model Methanogenic Archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A

Many archaeal cell envelopes contain a protein coat or sheath composed of one or more surface exposed proteins. These surface layer (S-layer) proteins contribute structural integrity and protect the lipid membrane from environmental challenges. To explore the species diversity of these layers in the Methanosarcinaceae, the major S-layer protein in Methanosarcina barkeri strain Fusaro was identified using proteomics. The Mbar_A1758 gene product was present in multiple forms with apparent sizes of 130, 120, and 100 kDa, consistent with post-translational modifications including signal peptide excision and protein glycosylation. A protein with features related to the surface layer proteins found in Methanosarcina acetivorans C2A and Methanosarcina mazei Goel was identified in the M. barkeri genome. These data reveal a distinct conserved protein signature with features and implied cell surface architecture in the Methanosarcinaceae that is absent in other archaea. Paralogous gene expression patterns in two Methanosarcina species revealed abundant expression of a single S-layer paralog in each strain. Respective promoter elements were identified and shown to be conserved in mRNA coding and upstream untranslated regions. Prior M. acetivorans genome annotations assigned S-layer or surface layer associated roles of eighty genes: however, of 68 examined none was significantly expressed relative to the experimentally determined S-layer gene

Microwave Components with MEMS Switches

RF MEMS switches with metal-metal contacts are being developed for microwave applications where broadband, high linearity performance is required. These switches provide less than 0.2 dB insertion loss through 40 GHz. This paper describes the integration of these switches into selected microwave components such as reconfigurable antenna elements, tunable filters, switched delay lines, and SPDT switches. Microwave and millimeter wave measured results from these circuits are presented

The evaluation of Computed Tomography hard- and software tools for micropaleontologic studies on foraminifera

Foraminifera (Forams) are single-celled amoeba-like organisms in the sea, which build a tiny calcareous multi-chambered shell for protection. Their enormous abundance, great variation of shape through time and their presence in all marine deposits made these tiny microfossils the oil companies’ best friend by facilitating the detection of new oil wells. Besides the success of forams in the oil and gas industry, they are also a most powerful tool for reconstructing climate change in the past. The shell of a foraminifer is a tiny gold mine of information both geometrical as chemical. However, until recently the best information on this architecture was only obtained through imaging the outside of a shell with Scanning Electron Microscopy (SEM), giving no clues towards internal structures other than single snapshots through breaking a specimen apart. With X-ray computed tomography (CT) it is possible to overcome this problem and uncover a huge amount of geometrical information without destructing the samples. Using the last generation of micro-CT’s, called nano-CT, because of the sub-micron resolution, it is now possible to perform adequate imaging even on these tiny samples without needing huge facilities. In this research, a comparison is made between different X-ray sources and X-ray detectors and the resulting image resolution. Both sharpness, noise and contrast are very important parameters that will have important effects on the accuracy of the results and on the speed of data-processing. Combining this tomography technique with specific image processing software, called segmentation, it is possible to obtain a 3D virtual representation of the entire forams shell. This 3D virtual object can then be used for many purposes, from which automatic measurement of the chambers size is one of the most important ones. The segmentation process is a combination of several algorithms that are often used in CT evaluation, in this work an evaluation of those algorithms is presented. Difficulties arising when the forams shell is filled with material but it still remains possible to perform adequate segmentation. The void inside the shell corresponds to the chambers of the foram and the inter-chamber connections. Using automatic separation algorithms it is possible to obtain the shape of individual chambers. The results from the segmentation process can then be used to perform a multitude of analysis on each foram. Out of the shells geometry one can derive variations in shell thickness, shell density and shell porosity. Since the geometry of each individual chamber can be derived, it is possible to track chamber size variation for one foram or between two different forams, the difference in orientation and distance between the chambers. In this work the algorithms and procedures have been applied on two forams: A. Pseudouvigerina sp., a benthic foram that lived within the sediments at the seafloor. It dates from the earliest Paleocene, 65 Ma and was collected near Brazos River, Texas. B. Globigerinoides, a modern planktic foram, living in the upper part of the water comlumn in the open ocean. The test settled on the seafloor after death and was recently collected from the seafloor at 2900 m water depth at Nazca Ridge in the eastern Pacific Ocean. It was found that foram A consists of 15 chambers with a total volume of 1.8 x 106 µm³ and shows progressive growth of consecutive chambers (average of 1,5 magnification). After the large globular initial chamber, which indicates asexual reproduction, each chamber is slightly larger than the previous one. In the later stages the chambers develop lateral edges with a thickened margin, leading to a distinct triangular shape in cross section. Foram B on the other hand has a distinct trochospiral coil (like a snail), consisting of 16 chambers with a total volume of 91 x 106 µm³. The entire shell thickens with every successive chamber, so that the initial part of the test is embraced in a thick calcite crust. The chambers grow rapidly in size (average magnification of 2,24 ), which is typical for most planktic foraminifera. The globular shape aids in the buoyancy of the specimen for its planktic way of life

Progressive fault isolation and grid restoration strategy for MTDC networks

A multi-terminal dc (MTDC) grid has a number of advantages over traditional ac transmission. However, dc protection is still one of the main technical issues holding back the expansion of point-to-point dc links to MTDC networks. Most dc protection strategies are based on dc circuit breakers (DCCBs); however, DCCBs are still under development and their arrival to the market will come at an unclear time and cost. Conversely, ac circuit breakers (ACCBs) are readily available and represent a more economic alternative to protect dc networks. Following this line, a protection strategy for MTDC grids is proposed in this paper. This uses ACCBs for dc fault current clearing and fast dc disconnectors for fault isolation. The faulty link is correctly discriminated and isolated while communication links are not required. This strategy contributes to a reduced network outage period as the non-faulty links are out of operation for a relatively short period of time and are restored in a progressive manner. The effectiveness of the proposed strategy is tested in PSCAD/EMTDC for pole-to-ground and pole-to-pole faults

Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.

UnlabelledSyntrophus aciditrophicus is a model syntrophic bacterium that degrades key intermediates in anaerobic decomposition, such as benzoate, cyclohexane-1-carboxylate, and certain fatty acids, to acetate when grown with hydrogen-/formate-consuming microorganisms. ATP formation coupled to acetate production is the main source for energy conservation by S. aciditrophicus However, the absence of homologs for phosphate acetyltransferase and acetate kinase in the genome of S. aciditrophicus leaves it unclear as to how ATP is formed, as most fermentative bacteria rely on these two enzymes to synthesize ATP from acetyl coenzyme A (CoA) and phosphate. Here, we combine transcriptomic, proteomic, metabolite, and enzymatic approaches to show that S. aciditrophicus uses AMP-forming, acetyl-CoA synthetase (Acs1) for ATP synthesis from acetyl-CoA. acs1 mRNA and Acs1 were abundant in transcriptomes and proteomes, respectively, of S. aciditrophicus grown in pure culture and coculture. Cell extracts of S. aciditrophicus had low or undetectable acetate kinase and phosphate acetyltransferase activities but had high acetyl-CoA synthetase activity under all growth conditions tested. Both Acs1 purified from S. aciditrophicus and recombinantly produced Acs1 catalyzed ATP and acetate formation from acetyl-CoA, AMP, and pyrophosphate. High pyrophosphate levels and a high AMP-to-ATP ratio (5.9 ± 1.4) in S. aciditrophicus cells support the operation of Acs1 in the acetate-forming direction. Thus, S. aciditrophicus has a unique approach to conserve energy involving pyrophosphate, AMP, acetyl-CoA, and an AMP-forming, acetyl-CoA synthetase.ImportanceBacteria use two enzymes, phosphate acetyltransferase and acetate kinase, to make ATP from acetyl-CoA, while acetate-forming archaea use a single enzyme, an ADP-forming, acetyl-CoA synthetase, to synthesize ATP and acetate from acetyl-CoA. Syntrophus aciditrophicus apparently relies on a different approach to conserve energy during acetyl-CoA metabolism, as its genome does not have homologs to the genes for phosphate acetyltransferase and acetate kinase. Here, we show that S. aciditrophicus uses an alternative approach, an AMP-forming, acetyl-CoA synthetase, to make ATP from acetyl-CoA. AMP-forming, acetyl-CoA synthetases were previously thought to function only in the activation of acetate to acetyl-CoA

Psychiatric comorbidity and causal disease models

In psychiatry, comorbidity is the rule rather than the exception. Up to 45% of all patients are classified as having more than one psychiatric disorder. These high rates of comorbidity have led to a debate concerning the interpretation of this phenomenon. Some authors emphasize the problematic character of the high rates of comorbidity because they indicate absent zones of rarities. Others consider comorbid conditions to be a validator for a particular reclassification of diseases. In this paper we will show that those at first sight contrasting interpretations of comorbidity are based on similar assumptions about disease models. The underlying ideas are that firstly high rates of comorbidity are the result of the absence of causally defined diseases in psychiatry, and second that causal disease models are preferable to non-causal disease models. We will argue that there are good reasons to seek after causal understanding of psychiatric disorders, but that causal disease models will not rule out high rates of comorbidity-neither in psychiatry, nor in medicine in general. By bringing to the fore these underlying assumptions, we hope to clear the ground for a different understanding of comorbidity, and of models for psychiatric diseases. (C) 2012 Elsevier Inc. All rights reserved.</p

Strain Hardening of Polymer Glasses: Entanglements, Energetics, and Plasticity

Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While stress-strain curves for a wide range of temperature can be fit to the functional form predicted by entropic network models, many other results are fundamentally inconsistent with the physical picture underlying these models. Stresses are too large to be entropic and have the wrong trend with temperature. The most dramatic hardening at large strains reflects increases in energy as chains are pulled taut between entanglements rather than a change in entropy. A weak entropic stress is only observed in shape recovery of deformed samples when heated above the glass transition. While short chains do not form an entangled network, they exhibit partial shape recovery, orientation, and strain hardening. Stresses for all chain lengths collapse when plotted against a microscopic measure of chain stretching rather than the macroscopic stretch. The thermal contribution to the stress is directly proportional to the rate of plasticity as measured by breaking and reforming of interchain bonds. These observations suggest that the correct microscopic theory of strain hardening should be based on glassy state physics rather than rubber elasticity.Comment: 15 pages, 12 figures: significant revision

Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions

We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein–protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability