Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software

Aim To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors. Method We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www. empop.org) by means of two mtDNA data sets that were submitted for quality control. Results The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data. Conclusion Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables

An In Depth Study into Using EMI Signatures for Appliance Identification

Energy conservation is a key factor towards long term energy sustainability. Real-time end user energy feedback, using disaggregated electric load composition, can play a pivotal role in motivating consumers towards energy conservation. Recent works have explored using high frequency conducted electromagnetic interference (EMI) on power lines as a single point sensing parameter for monitoring common home appliances. However, key questions regarding the reliability and feasibility of using EMI signatures for non-intrusive load monitoring over multiple appliances across different sensing paradigms remain unanswered. This work presents some of the key challenges towards using EMI as a unique and time invariant feature for load disaggregation. In-depth empirical evaluations of a large number of appliances in different sensing configurations are carried out, in both laboratory and real world settings. Insights into the effects of external parameters such as line impedance, background noise and appliance coupling on the EMI behavior of an appliance are realized through simulations and measurements. A generic approach for simulating the EMI behavior of an appliance that can then be used to do a detailed analysis of real world phenomenology is presented. The simulation approach is validated with EMI data from a router. Our EMI dataset - High Frequency EMI Dataset (HFED) is also released

Role of tyrosine M210 in the initial charge separation of reaction centers of Rhodobacter sphaeroides

Femtosecond spectroscopy was used in combination with site-directed mutagenesis to study the influence of tyrosine M210 (YM210) on the primary electron transfer in the reaction center of Rhodobacter sphaeroides. The exchange of YM210 to phenylalanine caused the time constant of primary electron transfer to increase from 3.5 f 0.4 ps to 16 f 6 ps while the exchange to leucine increased the time constant even more to 22 f 8 ps. The results suggest that tyrosine M210 is important for the fast rate of the primary electron transfer

Correlation of structural and spectroscopic properties of a photosynthetic reaction center

Polarized spectra of absorption and light-induced absorbance changes are presented for the crystallized reaction centers of Rhodopseudomonas viridis. We find that a model based on extended dipole interaction between all six pigments is capable of interpreting detailed features such as the contributions from the individual pigments to the various absorption peaks. Even though the pigments are arranged in approximate C2 symmetry, the optical spectra together with the calculations reflect deviations from this symmetry, which may be important in understanding the electron pathway

Temperature dependence of the primary electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides

The primary electron transfer (ET) in reaction centers (RC) of Rhodobacter sphaeroides is investigated as a function of temperature with femtosecond time resolution. For temperatures from 300 to 25 K the ET to the bacteriopheophytin is characterized by a biphasic time dependence. The two time constants of τ1=3.5±0.4 ps and τ2=1.2±0.3 ps at T=300 K decrease continously with temperature to values of τ1=1.4±0.3 ps and τ2=0.3±0.15 ps at 25 K. The experimental results indicate that the ET is not thermally activated and that the same ET mechanisms are active at room and low temperatures. All observations are readily rationalized by a two-step ET model with the monomeric bacteriochlorophyll as a real electron carrier

Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East

<p>Abstract</p> <p>Background</p> <p>Nearly half of the West Eurasian assemblage of human mitochondrial DNA (mtDNA) is fractioned into numerous sub-lineages of the predominant haplogroup (hg) R0. Several hypotheses have been proposed on the origin and the expansion times of some R0 sub-lineages, which were partially inconsistent with each other. Here we describe the phylogenetic structure and genetic variety of hg R0 in five European populations and one population from the Middle East.</p> <p>Results</p> <p>Our analysis of 1,350 mtDNA haplotypes belonging to R0, including entire control region sequences and 45 single nucleotide polymorphisms from the coding region, revealed significant differences in the distribution of different sub-hgs even between geographically closely located regions. Estimates of coalescence times that were derived using diverse algorithmic approaches consistently affirmed that the major expansions of the different R0 hgs occurred in the terminal Pleistocene and early Holocene.</p> <p>Conclusion</p> <p>Given an estimated coalescence time of the distinct lineages of 10 – 18 kya, the differences in the distributions could hint to either limited maternal gene flow after the Last Glacial Maximum due to the alpine nature of the regions involved or to a stochastic loss of diversity due to environmental events and/or disease episodes occurred at different times and in distinctive regions. Our comparison of two different ways of obtaining the timing of the most recent common ancestor confirms that the time of a sudden expansion can be adequately recovered from control region data with valid confidence intervals. For reliable estimates, both procedures should be applied in order to cross-check the results for validity and soundness.</p

Detailed studies of the subpicosecond kinetics in the primary electron transfer of reaction centers of Rhodopseudomonas viridis

The primary, light-induced charge separation in reaction centers of Rhodopseudomonas viridis is investigated with femtosecond time resolution. The absorption changes after direct excitation of the primary donor P at 955 nm are investigated in the time range from 100 fs to 600 ps. The experimental data, taken at various probing wavelengths, reveal one subpicosecond and two picosecond time constants: 0.65 ± 0.2 ps, 3.5 ± 0.4 ps, and 200 ± 20 ps. The previously undetected 0.65 ps kinetics can be observed clearly in the spectral range of the Qx and Qy transitions of the monomeric bacteriochlorophylls. The experimental data support the idea that the accessory bacteriochlorophyll B A participates in the electron-transfer process. Reference