Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal (2019), doi:10.1038/s41396-019-0373-4.The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich

The Measurement Calculus

Measurement-based quantum computation has emerged from the physics community as a new approach to quantum computation where the notion of measurement is the main driving force of computation. This is in contrast with the more traditional circuit model which is based on unitary operations. Among measurement-based quantum computation methods, the recently introduced one-way quantum computer stands out as fundamental. We develop a rigorous mathematical model underlying the one-way quantum computer and present a concrete syntax and operational semantics for programs, which we call patterns, and an algebra of these patterns derived from a denotational semantics. More importantly, we present a calculus for reasoning locally and compositionally about these patterns. We present a rewrite theory and prove a general standardization theorem which allows all patterns to be put in a semantically equivalent standard form. Standardization has far-reaching consequences: a new physical architecture based on performing all the entanglement in the beginning, parallelization by exposing the dependency structure of measurements and expressiveness theorems. Furthermore we formalize several other measurement-based models: Teleportation, Phase and Pauli models and present compositional embeddings of them into and from the one-way model. This allows us to transfer all the theory we develop for the one-way model to these models. This shows that the framework we have developed has a general impact on measurement-based computation and is not just particular to the one-way quantum computer.Comment: 46 pages, 2 figures, Replacement of quant-ph/0412135v1, the new version also include formalization of several other measurement-based models: Teleportation, Phase and Pauli models and present compositional embeddings of them into and from the one-way model. To appear in Journal of AC

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [C-13]bicarbonate, DNA-qSIP showed that ammoniaoxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural C-13-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [C-13] bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (> 50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [C-13] bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with C-13-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from "dark" primary production. IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ "dark" primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover

Duality invariance of non-anticommutative N=1/2 supersymmetric U(1) gauge theory

A parent action is introduced to formulate (S-) dual of non-anticommutative N=1\2 supersymmetric U(1) gauge theory. Partition function for parent action in phase space is utilized to establish the equivalence of partition functions of the theories which this parent action produces. Thus, duality invariance of non-anticommutative N=1\2 supersymmetric U(1) gauge theory follows. The results which we obtained are valid at tree level or equivalently at the first order in the nonanticommutativity parameter C_{\mu\nu}.Comment: 12 pages, some comments and references are added. To appear in JHE

Analyzing Complex Problem Solving by Dynamic Brain Networks

Complex problem solving is a high level cognitive task of the human brain, which has been studied over the last decade. Tower of London (TOL) is a game that has been widely used to study complex problem solving. In this paper, we aim to explore the underlying cognitive network structure among anatomical regions of complex problem solving and its subtasks, namely planning and execution. A new computational model for estimating a brain network at each time instant of fMRI recordings is proposed. The suggested method models the brain network as an Artificial Neural Network, where the weights correspond to the relationships among the brain anatomic regions. The first step of the model is preprocessing that manages to decrease the spatial redundancy while increasing the temporal resolution of the fMRI recordings. Then, dynamic brain networks are estimated using the preprocessed fMRI signal to train the Artificial Neural Network. The properties of the estimated brain networks are studied in order to identify regions of interest, such as hubs and subgroups of densely connected brain regions. The representation power of the suggested brain network is shown by decoding the planning and execution subtasks of complex problem solving. Our findings are consistent with the previous results of experimental psychology. Furthermore, it is observed that there are more hubs during the planning phase compared to the execution phase, and the clusters are more strongly connected during planning compared to execution

Interface Friction Parameters for the Mathematical Modeling of Shell Structures with Infill

Thin metal or reinforced concrete shells with granular infill structures are considered in this article. These structures are massive and they are used as support for the construction of berthing quays, piers, artificial islands, shore protection, and other structures of coastal infrastructure. It is more convenient to use the thin shell structures during the development of the Arctic shelf, because it is possible to install them from the ice side. In addition, it is possible to enhance the technology and install thin shells with infill on deeper solid foundation layers. A mathematical model for the stresses on a compressible foundation soil in front of a thin cylindrical shell with infill due to the eccentric loading is developed. A modeling and experimental determination of the interface strength of the contact surface between the infill and the inner surface of the shell is proposed. The details of the construction stages and testing of the physical model used for the experiments are discussed. The effects of the interface friction on the shell behavior and on the foundation stresses in front of the wall are investigated. The influence of parameters affecting the interaction between the soil infill and the inner surface of the shell material is determined. It is based on a comparison of experimental results with calculations performed using the proposed mathematical model. The obtained parameters and proposed methods can be used in numerical simulations using the finite element method to analyze and design the thin shell structures with soil infill. The findings of the study and proposed methods can also be applied to the thin shell structures used in other facilities such as hydraulic, industrial, civil, and transportation

Aktivnost arginaze u ovarijskim strukturama krava švicarske smeđe pasmine i njezinih križanaca.

Arginase is the last enzyme of the urea cycle. It catalyses the hydrolysis of L-arginine to L-ornitine and urea. The aim of this study was to investigate the presence of arginase activity in ovarian structures such as: Graaf follicles, GF (Medium and Large size, M- and L-size), Corpus Haemorrhagicum (CH), and various types of Corpus Luteum (CL) such as: cyclic CL (CCL), 2-4 month pregnancy CL (2-4 MCL) and 4-7 month pregnancy CL (4-7 MCL). Ovarian tissues of 62 cows (7-10 years old and Brown Swiss or its cross-breeds), collected from a local slaughterhouse, were used as material. The materials were divided into 6 experimental groups, as follows: MGF group (n = 7), LGF group (n = 21), CH group (n = 7), CCL group (n = 6), 2-4 MCL group (n = 9) and 4-7 MCL group (n = 12). Arginase activities were measured as 0.056 ± 0.017, 0.100 ± 0.016, 2.517 ± 0.521, 0.827 ± 0.190, 0.674 ± 0.106 and 0.833 ± 0.093 U/mg protein in all groups, respectively. Arginase activity in the CH group was significantly higher than that in the CCL, 2-4 MCL and 4-7 MCL groups (P<0.001). The lowest enzyme activity was in the MGF and LGF groups. Hence, it was concluded that the arginase enzyme might play a crucial role in cell division, proliferation and differentiation in the ovarian tissues (especially the CH) of mature cows.Arginaza je posljednji enzim u ciklusu ureje koji katalizira hidrolizu L-arginina u L-ornitin i ureju. Cilj istraživanja bio je utvrditi prisutnost aktivnosti arginaze u ovarijskim strukturama kao što su Graafovi folikuli, GF (srednje veliki - M i veliki - L), corpus haemorrhagicum (CH) i različiti tipovi corpus luteum (CL) kao što su ciklični (CCL), 2-4 mjeseca graviditetni (2-4 MCL) i 4-7 mjeseci graviditetni (4-7 MCL). Tkiva ovarija od 62 krave (švicarske smeđe pasmine i križanaca u dobi od 7 do 10 godina) prikupljena su u lokalnoj klaonici. Materijali su bili podijeljeni u 6 pokusnih skupina kako slijedi: MGF skupina (n = 7), LGF skupina (n = 21), CH skupina (n = 7), CCL skupina (n = 6), 2-4 MCL skupina (n = 9) i 4-7 MCL skupina (n = 12). Slijedom navedenih skupina, aktivnost arginaze bila je 0,056 ± 0,017, 0,100 ± 0,016, 2,517 ± 0,521, 0,827 ± 0,190, 0,674 ± 0,106 i 0,833 ± 0,093 U/mg. Aktivnost arginaze u CH skupini bila je signifikantno viša u odnosu na skupine CCL, 2-4 MCL i 4-7 MCL (P<0,001). Najniža aktivnost enzima bila je u skupinama MGF i LGF. Zaključeno je o mogućoj ključnoj ulozi aktivnosti enzima arginaze u diobi stanica, proliferaciji i diferencijaciji ovarijskih tkiva (osobito CH) kod odraslih krava

Acquired Generalized Lipodystrophy Associated with Autoimmune Hepatitis and Low Serum C4 Level

Lipodystrophies are a group of diseases characterized by loss of fat tissue and are associated with insulin resistance. A six-year- old girl followed with the diagnosis of autoimmune hepatitis showed a severe loss of fat tissue, hyperinsulinemia, impaired glucose tolerance, hypertriglyceridemia and low serum complement 4 (C4) levels. She had coarse facial features with generalized loss of subcutaneous fat and prominent muscularity. Remarkable acanthosis nigricans was present over the neck, axilla, and umbilicus. Two hours after glucose loading, the glucose tolerance test revealed a glucose level of 258 mg/dL, a HbA1c value of 6.8%, and an insulin level of 642.9 mIU/mL, documenting a state of insulin resistance and type 2 diabetes mellitus. Acquired generalized lipodystrophy was diagnosed and metformin with dietary intervention was initiated. Low serum complement levels proved the autoimmune nature of the process. We conclude that the serum complement levels must be investigated in patients with acquired lipodystrophy, particularly when it is associated with autoimmune hepatitis