Combinatorial chromophore assembly inside a DNA four-way junction

In 1964 first proposed by Robin Holliday as a mechanistic model to solve the mystery of how genetic information is exchanged in yeast, the DNA four-way junction or Holliday junction (HJ) was proofed to be the key in- termediate in homologous recombination and became an important tool in the field of DNA origami, computation and nanomachines. Herein we use the assembly of four modified nucleic acid strands into the planar square conformation of this higher order DNA structure to demonstrate in a proof of principle manner the cumulative effect of pyrene moieties interacting inside the junction.[1][2]

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

Self-motion perception influences number processing: evidence from a parity task

We investigated the role of horizontal body motion on the processing of numbers. We hypothesized that leftward self-motion leads to shifts in spatial attention and therefore facilitates the processing of small numbers, and vice versa, we expected that rightward self-motion facilitates the processing of large numbers. Participants were displaced by means of a motion platform during a parity judgment task. We found a systematic influence of self-motion direction on number processing, suggesting that the processing of numbers is intertwined with the processing of self-motion perception. The results differed from known spatial numerical compatibility effects in that self-motion exerted a differential influence on inner and outer numbers of the given interval. The results highlight the involvement of sensory body motion information in higher-order spatial cognition.

Moving along the mental time line influences the processing of future related words

Abstract concepts like numbers or time are thought to be represented in the more concrete domain of space and the sensorimotor system. For example, thinking of past or future events has a physical manifestation in backward or forward body sway, respectively. In the present study, we investigated the reverse effect: can passive whole-body motion influence the processing of temporal information? Participants were asked to categorize verbal stimuli to the concepts future or past while they were displaced forward and backward (Experiment 1), or upward and downward (Experiment 2). The results showed that future related verbal stimuli were categorized faster during forward as compared to backward motion. This finding supports the view that temporal events are represented along a mental time line and that the sensorimotor system is linked to that representation. We showed that body motion is not just an epiphenomenon of temporal thoughts. Passive whole-body motion can influence higher-order temporal cognition.

Stress and hemostasis: an update

Numerous naturalistic, experimental, and mechanistic studies strongly support the notion that-as part of fight-or-flight response-hemostatic responses to acute psychosocial stress result in net hypercoagulability, which would protect a healthy organism from bleeding in case of injury. Sociodemographic factors, mental states, and comorbidities are important modulators of the acute prothrombotic stress response. In patients with atherosclerosis, exaggerated and prolonged stress-hypercoagulability might accelerate coronary thrombus growth following plaque rupture. Against a background risk from acquired prothrombotic conditions and inherited thrombophilia, acute stress also might trigger venous thromboembolic events. Chronic stressors such as job strain, dementia caregiving, and posttraumatic stress disorder as well as psychological distress from depressive and anxiety symptoms elicit a chronic low-grade hypercoagulable state that is no longer viewed as physiological but might impair vascular health. Through activation of the sympathetic nervous system, higher order cognitive processes and corticolimbic brain areas shape the acute prothrombotic stress response. Hypothalamic-pituitary-adrenal axis and autonomic dysfunction, including vagal withdrawal, are important regulators of hemostatic activity with longer lasting stress. Randomized placebo-controlled trials suggest that several cardiovascular drugs attenuate the acute prothrombotic stress response. Behavioral interventions and psychotropic medications might mitigate chronic low-grade hypercoagulability in stressed individuals, but further studies are clearly needed. Restoring normal hemostatic function with biobehavioral interventions bears the potential to ultimately decrease the risk of thrombotic diseases.

Jazz drummers recruit language-specific areas for the processing of rhythmic structure

Rhythm is a central characteristic of music and speech, the most important domains of human communication using acoustic signals. Here, we investigated how rhythmical patterns in music are processed in the human brain, and, in addition, evaluated the impact of musical training on rhythm processing. Using fMRI, we found that deviations from a rule-based regular rhythmic structure activated the left planum temporale together with Broca's area and its right-hemispheric homolog across subjects, that is, a network also crucially involved in the processing of harmonic structure in music and the syntactic analysis of language. Comparing the BOLD responses to rhythmic variations between professional jazz drummers and musical laypersons, we found that only highly trained rhythmic experts show additional activity in left-hemispheric supramarginal gyrus, a higher-order region involved in processing of linguistic syntax. This suggests an additional functional recruitment of brain areas usually dedicated to complex linguistic syntax processing for the analysis of rhythmical patterns only in professional jazz drummers, who are especially trained to use rhythmical cues for communication.

Cardiolipin membrane domains in prokaryotes and eukaryotes.

Cardiolipin (CL) plays a key role in dynamic organization of bacterial and mitochondrial membranes. CL forms membrane domains in bacterial cells, and these domains appear to participate in binding and functional regulation of multi-protein complexes involved in diverse cellular functions including cell division, energy metabolism, and membrane transport. Visualization of CL domains in bacterial cells by the fluorescent dye 10-N-nonyl acridine orange is critically reviewed. Possible mechanisms proposed for CL dynamic localization in bacterial cells are discussed. In the mitochondrial membrane CL is involved in organization of multi-subunit oxidative phosphorylation complexes and in their association into higher order supercomplexes. Evidence suggesting a possible role for CL in concert with ATP synthase oligomers in establishing mitochondrial cristae morphology is presented. Hypotheses on CL-dependent dynamic re-organization of the respiratory chain in response to changes in metabolic states and CL dynamic re-localization in mitochondria during the apoptotic response are briefly addressed.

Neural analogs of associative learning in {\it Aplysia\/}: Experimental and theoretical approaches

A change in synaptic strength arising from the activation of two neuronal pathways at approximately the same time is a form of associative plasticity and may underlie classical conditioning. Previously, a cellular analog of a classical conditioning protocol has been demonstrated to produce short-term associative plasticity at the connections between sensory and motor neurons in Aplysia. A similar training protocol produced long-term (24 hour) enhancement of excitatory postsynaptic potentials (EPSPs). EPSPs produced by sensory neurons in which activity was paired with a reinforcing stimulus were significantly larger than unpaired controls 24 hours after training. To examined whether the associative plasticity observed at these synapses may be involved in higher-order forms of classical conditioning, a neural analog of contingency was developed. In addition, computer simulations were used to analyze whether the associative plasticity observed in Aplysia could, in theory, account for second-order conditioning and blocking. ^

Studies of subcellular localization and complex formation of the Agrobacterium tumefaciens transport ATPase VirB11

The VirB11 ATPase is an essential component of an Agrobacterium tumefaciens type IV bacterial secretion system that transfers oncogenic nucleoprotein complexes to susceptible plant cells. This dissertation investigates the subcellular localization and homo-oligomeric state of the VirB11 ATPase in order to provide insights about the assembly of the protein as a subunit of this membrane-associated transfer system. Subcellular fractionation studies and quantitative immunoblot analysis demonstrated that $\sim$30% of VirB11 partitioned as soluble protein and $\sim$70% was tightly associated with the bacterial cytoplasmic membrane. No differences were detected in VirB11 subcellular localization and membrane association in the presence or absence of other transport system components. Mutations in virB11 affecting protein function were mapped near the amino terminus, just upstream of a region encoding a Walker 'A' nucleotide-binding site, and within the Walker 'A' motif partitioned almost exclusively with the cytoplasmic membrane, suggesting that an activity associated with nucleotide binding could modulate the affinity of VirB11 for the cytoplasmic membrane. Merodiploid analysis of VirB11 mutant and truncation derivatives provided strong evidence that VirB11 functions as a homo- or heteromultimer and that the C-terminal half of VirB11 contains a protein interaction domain. A combination of biochemical and molecular genetic approaches suggested that VirB11 and the green fluorescence protein (GFP) formed a mixed multimer as demonstrated by immunoprecipitation experiments with anti-GFP antibodies. Second, a hybrid protein composed of VirB11 fused to the N-terminal DNA-binding domain of bacteriophage $\lambda$ cI repressor conferred immunity to $\lambda$ superinfection, demonstrating that VirB11 self-association promotes dimerization of the chimeric repressor. A conserved Walker 'A' motif, though required for VirB11 function in T-complex export, was not necessary for VirB11 self-association. Sequences in both the N- and the C-terminal halves of the protein were found to contribute to self-association of the full length protein. Chemical cross-linking experiments with His$\sb6$ tagged VirB11 suggested that VirB11 probably assembles into a higher order homo-oligomeric complex. ^

Personality dimensions in persons symptomatically at risk of psychosis: pronounced but lacking a characteristic profile

AIM Personality dimensions are frequently abnormal in psychosis. We examined if these abnormalities form a personality profile that is characteristic for patients symptomatically at risk of psychosis. METHODS Four higher order personality dimensions were assessed in 104 at-risk patients, 67 clinical and 97 healthy controls with the 'Dimensional Assessment of Personality Pathology', and analysed by two-step cluster procedure to detect personality profiles. Logistic regression was used to test for predictors of profile assignment. RESULTS Low and high scorers were distinguished by two profiles. Patients were more likely high scorers. The presence of clinically relevant depression, though equally frequent in clinical groups, best predicted high scorers among patients. CONCLUSIONS Though at-risk patients were significantly more often high scorers, this seemed to be a general reflection of the level of psychopathology rather than a group characteristic. Thus, personality dimensions might be of little value for facilitating early detection but might be important to consider in early intervention approaches.

Bounds for the probability generating functional of a Gibbs point process

We derive explicit lower and upper bounds for the probability generating functional of a stationary locally stable Gibbs point process, which can be applied to summary statistics such as the F function. For pairwise interaction processes we obtain further estimates for the G and K functions, the intensity, and higher-order correlation functions. The proof of the main result is based on Stein's method for Poisson point process approximation.

Balancing the mind: vestibular induced facilitation of egocentric mental transformations

The body schema is a key component in accomplishing egocentric mental transformations, which rely on bodily reference frames. These reference frames are based on a plurality of different cognitive and sensory cues among which the vestibular system plays a prominent role. We investigated whether a bottom-up influence of vestibular stimulation modulates the ability to perform egocentric mental transformations. Participants were significantly faster to make correct spatial judgments during vestibular stimulation as compared to sham stimulation. Interestingly, no such effects were found for mental transformation of hand stimuli or during mental transformations of letters, thus showing a selective influence of vestibular stimulation on the rotation of whole-body reference frames. Furthermore, we found an interaction with the angle of rotation and vestibular stimulation demonstrating an increase in facilitation during mental body rotations in a direction congruent with rightward vestibular afferents. We propose that facilitation reflects a convergence in shared brain areas that process bottom-up vestibular signals and top-down imagined whole-body rotations, including the precuneus and tempero-parietal junction. Ultimately, our results show that vestibular information can influence higher-order cognitive processes, such as the body schema and mental imagery.

Coherence and phase locking in the scalp EEG and between LORETA model sources, and microstates as putative mechanisms of brain temporo-spatial functional organization

Brain electric mechanisms of temporary, functional binding between brain regions are studied using computation of scalp EEG coherence and phase locking, sensitive to time differences of few milliseconds. However, such results if computed from scalp data are ambiguous since electric sources are spatially oriented. Non-ambiguous results can be obtained using calculated time series of strength of intracerebral model sources. This is illustrated applying LORETA modeling to EEG during resting and meditation. During meditation, time series of LORETA model sources revealed a tendency to decreased left-right intracerebral coherence in the delta band, and to increased anterior-posterior intracerebral coherence in the theta band. An alternate conceptualization of functional binding is based on the observation that brain electric activity is discontinuous, i.e., that it occurs in chunks of up to about 100 ms duration that are detectable as quasi-stable scalp field configurations of brain electric activity, called microstates. Their functional significance is illustrated in spontaneous and event-related paradigms, where microstates associated with imagery- versus abstract-type mentation, or while reading positive versus negative emotion words showed clearly different regions of cortical activation in LORETA tomography. These data support the concept that complete brain functions of higher order such as a momentary thought might be incorporated in temporal chunks of processing in the range of tens to about 100 ms as quasi-stable brain states; during these time windows, subprocesses would be accepted as members of the ongoing chunk of processing.

Elucidation of Nucleic Acid–Drug Interactions by Tandem Mass Spectrometry

In continuation of the long tradition of mass spectrometric research at the University of Bern, our group focuses on the characterization of nucleic acids as therapeutic agents and as drug targets. This article provides a short overview of our recent work on platinated single-stranded and higher-order nucleic acids. Nearly three decades ago the development of soft ionization techniques opened a whole new chapter in the mass spectrometric analysis of not only nucleic acids themselves, but also their interactions with potential drug candidates. In contrast to modern next generation sequencing approaches, though, the goal of the tandem mass spectrometric investigation of nucleic acids is by no means the complete sequencing of genetic DNA, but rather the characterization of short therapeutic and regulatory oligonucleotides and the elucidation of nucleic acid–drug interactions. The influence of cisplatin binding on the gas-phase dissociation of nucleic acids was studied by the means of electrospray ionization tandem mass spectrometry. Experiments on native and modified DNA and RNA oligomers confirmed guanine base pairs as the preferred platination site and laid the basis for the formulation of a gas-phase fragmentation mechanism of platinated oligonucleotides. The study was extended to double stranded DNA and DNA quadruplexes. While duplexes are believed to be the main target of cisplatin in vivo, the recently discovered DNA quadruplexes constitute another promising target for anti-tumor drugs owing to their regulatory functions in the cell cycle.

GOCE: assessment of GPS-only gravity field determination

The GOCE satellite was orbiting the Earth in a Sun-synchronous orbit at a very low altitude for more than 4 years. This low orbit and the availability of high-quality data make it worthwhile to assess the contribution of GOCE GPS data to the recovery of both the static and time-variable gravity fields. We use the kinematic positions of the official GOCE precise science orbit (PSO) product to perform gravity field determination using the Celestial Mechanics Approach. The generated gravity field solutions reveal severe systematic errors centered along the geomagnetic equator. Their size is significantly coupled with the ionospheric density and thus generally increasing over the mission period. The systematic errors may be traced back to the kinematic positions of the PSO product and eventually to the ionosphere-free GPS carrier phase observations used for orbit determination. As they cannot be explained by the current higher order ionospheric correction model recommended by the IERS Conventions 2010, an empirical approach is presented by discarding GPS data affected by large ionospheric changes. Such a measure yields a strong reduction of the systematic errors along the geomagnetic equator in the gravity field recovery, and only marginally reduces the set of useable kinematic positions by at maximum 6 % for severe ionosphere conditions. Eventually it is shown that GOCE gravity field solutions based on kinematic positions have a limited sensitivity to the largest annual signal related to land hydrology.