Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions

The Gram-stain-negative, oxidase negative, catalase positive strain KPC-SM-21T, isolated from a digestate of a storage tank of a mesophilic German biogas plant, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the nearly full-length 16S rRNA gene revealed highest gene sequence similarity to Acinetobacter baumannii ATCC 19606T (97.0%). Phylogenetic trees calculated based on partial rpoB and gyrB gene sequences showed a distinct clustering of strain KPC-SM-21T with Acinetobacter gerneri DSM 14967T = CIP 107464T and not with A. baumannii, which was also supported in the five housekeeping genes multilocus sequence analysis based phylogeny. Average nucleotide identity values between whole genome sequences of strain KPC-SM-21T and next related type strains supported the novel species status. The DNA G + C content of strain KPC-SM-21T was 37.7 mol%. Whole-cell MALDI-TOF MS analysis supported the distinctness of the strain to type strains of next related Acinetobacter species. Predominant fatty acids were C18:1 ω9c (44.2%), C16:0 (21.7%) and a summed feature comprising C16:1 ω7c and/or iso-C15:0 2-OH (15.3%). Based on the obtained genotypic, phenotypic and chemotaxonomic data we concluded that strain KPC-SM-21T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter stercoris sp. nov. is proposed. The type strain is KPC-SM-21T (= DSM 102168T = LMG 29413T).Peer Reviewe

A novel cell-free mitochondrial fusion assay amenable for high-throughput screenings of fusion modulators

Abstract Background Mitochondria are highly dynamic organelles whose morphology and position within the cell is tightly coupled to metabolic function. There is a limited list of essential proteins that regulate mitochondrial morphology and the mechanisms that govern mitochondrial dynamics are poorly understood. However, recent evidence indicates that the core machinery that governs mitochondrial dynamics is linked within complex intracellular signalling cascades, including apoptotic pathways, cell cycle transitions and nuclear factor kappa B activation. Given the emerging importance of mitochondrial plasticity in cell signalling pathways and metabolism, it is essential that we develop tools to quantitatively analyse the processes of fission and fusion. In terms of mitochondrial fusion, the field currently relies upon on semi-quantitative assays which, even under optimal conditions, are labour-intensive, low-throughput and require complex imaging techniques. Results In order to overcome these technical limitations, we have developed a new, highly quantitative cell-free assay for mitochondrial fusion in mammalian cells. This assay system has allowed us to establish the energetic requirements for mitochondrial fusion. In addition, our data reveal a dependence on active protein phosphorylation for mitochondrial fusion, confirming emerging evidence that mitochondrial fusion is tightly integrated within the global cellular response to signaling events. Indeed, we have shown that cytosol derived from cells stimulated with different triggers either enhance or inhibit the cell-free fusion reaction. Conclusions The adaptation of this system to high-throughput analysis will provide an unprecedented opportunity to identify and characterize novel regulatory factors. In addition, it provides a framework for a detailed mechanistic analysis of the process of mitochondrial fusion and the various axis of regulation that impinge upon this process in a wide range of cellular conditions. See Commentary: http://www.biomedcentral.com/1741-7007/8/9

CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs

Mitochondria are essential organelles that host crucial metabolic pathways and produce adenosine triphosphate. The mitochondrial proteome is heterogeneous among tissues and can dynamically change in response to different metabolic conditions. Although the transcriptional programs that govern mitochondrial biogenesis and respiratory function are well known, posttranscriptional regulatory mechanisms remain unclear. In this study, we show that the cytosolic RNA-binding protein clustered mitochondria homologue (CLUH) regulates the expression of a mitochondrial protein network supporting key metabolic programs required under nutrient deprivation. CLUH exerts its function by controlling the stability and translation of target messenger RNAs. In the absence of Cluh, mitochondria are severely depleted of crucial enzymes involved in catabolic energy-converting pathways. CLUH preserves oxidative mitochondrial function and glucose homeostasis, thus preventing death at the fetal–neonatal transition. In the adult liver, CLUH ensures maximal respiration capacity and the metabolic response to starvation. Our results shed new light on the posttranscriptional mechanisms controlling the expression of mitochondrial proteins and suggest novel strategies to tailor mitochondrial function to physiological and pathological conditions.Peer reviewe

Hochauflösende Detektion von Ordnung in Rydberg Vielteilchensystemen

Rydberg Atome sind auf Grund ihrer starken und kontrollierbaren Wechselwirkungen gut geeignet zur Quantensimulation von lang-reichweitig wechelwirkenden Systemen mit ultrakalten Atomen in optischen Gittern. In dieser Arbeit wird die Präparation und hochauflösende Abbildung von Rydberg Vielteilchensystemen demonstriert und die spontane Entstehung selbst-organisierter Ordnung beobachtet. In einer ersten Reihe von Experimenten wird die Ordnung in den post-selektierten Komponenten hoher Anregungsdichte bei hoher Temperatur untersucht. Die räumliche Konfiguration der Rydberg-Atome wird mit einer neuartigen Abbildungsmethode detektiert, die es ermöglicht die Position der individuellen Rydberg-Atome im Gitter durch Fluoreszenzabbildung der ehemaligen Rydberg-Atome nach dem Umpumpen in der Grundzustand zu bestimmen. Aus den gemessenen Rydberg-Positionen werden Korrelationsfunktionen berechnet und der Blockaderadius bestimmt. Für eine zweite Experimentreihe wird die Zeitabhängigkeit der optischen Kopplung an den Rydberg-Zustand kontrolliert. Zusammen mit der genauen Modellierung des Besetzungsmusters im optischen Gitter erlaubt dies die adiabatische Präparation von Rydberg Kristallen. Das System kann auch durch einen Ising Hamiltonian mit polynomialen Wechselwirkungen beschrieben werden, das diskutierte Szenario entspricht damit der Grundzustandspräparation in einem Quantenmagnet. Es werden Eigenschaften des kristallinen Grundzustands wie seine verschwindende Suszeptibilität und lokale Magnetisierungsdichten gemessen. Diese Arbeit stellt ein neue Stufe der Kontrolle über lang-reichweitig wechselwirkende Spin-Systeme dar und ebnet den Weg zur Quantensimulation mit Rydberg Atomen.Rydberg atoms are well-suited for the quantum simulation of long-range interacting Hamiltonians with ultracold atoms in optical lattices due to their strong and switchable interactions. In this thesis we demonstrate the preparation and high-resolution imaging of Rydberg many-body systems and observe the spontaneous emergence of self-organized ordering. In a first series of experiments we investigate the ordering in the post-selected high-excitation-density components of high-temperature many-body states. The spatial configuration of Rydberg atoms is imaged by a novel detection technique, which allows to determine the position of individual Rydberg atoms in the lattice by fluorescence imaging of the former Rydberg atoms after depumping them to the ground state. From the measured Rydberg atom positions we calculate correlation functions and determine the blockade radius. In a second set of experiments we implement time-dependent control of the optical coupling to the Rydberg state. Combined with the precise shaping of the initial atom pattern in the lattice this allows for the adiabatic preparation of Rydberg crystals. Via a mapping to an Ising Hamiltonian with power-law interactions this scenario corresponds to the ground state preparation in a quantum magnet. We measure properties of the crystalline ground state such as its vanishing susceptibility and local magnetization densities. This work demonstrates a new level of control over long-range interacting spin systems and paves the way for Rydberg-based quantum simulation

Improved Detection of Extended Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Input and Output Samples of German Biogas Plants by a Selective Pre-Enrichment Procedure

The presence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was investigated in input (manure from livestock husbandry) and output samples of six German biogas plants in 2012 (one sampling per biogas plant) and two German biogas plants investigated in an annual cycle four times in 2013/2014. ESBL-producing Escherichia coli were cultured by direct plating on CHROMagar ESBL from input samples in the range of 10 0 to 10 4 colony forming units (CFU) per g dry weight but not from output sample. This initially indicated a complete elimination of ESBL-producing E. coli by the biogas plant process. Detected non target bacteria were assigned to the genera Acinetobacter, Pseudomonas, Bordetella, Achromobacter, Castellaniella, and Ochrobactrum. A selective pre-enrichment procedure increased the detection efficiency of ESBL-producing E. coli in input samples and enabled the detection in five of eight analyzed output samples. In total 119 ESBL-producing E. coli were isolated from input and 46 from output samples. Most of the E. coli isolates carried CTX-M-type and/or TEM-type beta lactamases (94%), few SHV-type beta lactamase (6%). Sixty-four blaCTX-M genes were characterized more detailed and assigned mainly to CTX-M-groups 1 (85%) and 9 (13%), and one to group 2. Phylogenetic grouping of 80 E. coli isolates showed that most were assigned to group A (71%) and B1 (27%), only one to group D (2%). Genomic fingerprinting and multilocus sequence typing (MLST) showed a high clonal diversity with 41 BOX-types and 19 ST-types. The two most common ST-types were ST410 and ST1210. Antimicrobial susceptibility testing of 46 selected ESBL-producing E. coli revealed that several isolates were additionally resistant to other veterinary relevant antibiotics and some grew on CHROMagar STEC but shiga-like toxine (SLT) genes were not detected. Resistance to carbapenems was not detected. In summary the study showed for the first time the presence of ESBL-producing E. coli in output samples of German biogas plants