Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling

Previous work in yeast has suggested that modification of tRNAs, in particular uridine bases in the anticodon wobble position (U34), is linked to TOR (target of rapamycin) signaling. Hence, U34 modification mutants were found to be hypersensitive to TOR inhibition by rapamycin. To study whether this involves inappropriate TOR signaling, we examined interaction between mutations in TOR pathway genes (tip41Δ, sap190Δ, ppm1Δ, rrd1Δ) and U34 modification defects (elp3Δ, kti12Δ, urm1Δ, ncs2Δ) and found the rapamycin hypersensitivity in the latter is epistatic to drug resistance of the former. Epistasis, however, is abolished in tandem with a gln3Δ deletion, which inactivates transcription factor Gln3 required for TOR-sensitive activation of NCR (nitrogen catabolite repression) genes. In line with nuclear import of Gln3 being under control of TOR and dephosphorylation by the Sit4 phosphatase, we identify novel TOR-sensitive sit4 mutations that confer rapamycin resistance and importantly, mislocalise Gln3 when TOR is inhibited. This is similar to gln3Δ cells, which abolish the rapamycin hypersensitivity of U34 modification mutants, and suggests TOR deregulation due to tRNA undermodification operates through Gln3. In line with this, loss of U34 modifications (elp3Δ, urm1Δ) enhances nuclear import of and NCR gene activation (MEP2, GAP1) by Gln3 when TOR activity is low. Strikingly, this stimulatory effect onto Gln3 is suppressed by overexpression of tRNAs that usually carry the U34 modifications. Collectively, our data suggest that proper TOR signaling requires intact tRNA modifications and that loss of U34 modifications impinges on the TORsensitive NCR branch via Gln3 misregulation.

Stability of preconditioned finite volume schemes at low Mach numbers

In [4], Guillard and Viozat propose a finite volume method for the simulation of inviscid steady as well as unsteady flows at low Mach numbers, based on a preconditioning technique. The scheme satisfies the results of a single scale asymptotic analysis in a discrete sense and comprises the advantage that this can be derived by a slight modification of the dissipation term within the numerical flux function. Unfortunately, it can be observed by numerical experiments that the preconditioned approach combined with an explicit time integration scheme turns out to be unstable if the time step Dt does not satisfy the requirement to be O(M2) as the Mach number M tends to zero, whereas the corresponding standard method remains stable up to Dt=O(M), M to 0, which results from the well-known CFL-condition. We present a comprehensive mathematical substantiation of this numerical phenomenon by means of a von Neumann stability analysis, which reveals that in contrast to the standard approach, the dissipation matrix of the preconditioned numerical flux function possesses an eigenvalue growing like M-2 as M tends to zero, thus causing the diminishment of the stability region of the explicit scheme. Thereby, we present statements for both the standard preconditioner used by Guillard and Viozat [4] and the more general one due to Turkel [21]. The theoretical results are after wards confirmed by numerical experiments.

Micro-electromechanical structural design and optimization of vertical cavity photonic devices with wide continuous tuning

Diese Arbeit umfaßt das elektromechanische Design und die Designoptimierung von weit durchstimmbaren optischen multimembranbasierten Bauelementen, mit vertikal orientierten Kavitäten, basierend auf der Finiten Element Methode (FEM). Ein multimembran InP/Luft Fabry-Pérot optischer Filter wird dargestellt und umfassend analysiert. In dieser Arbeit wird ein systematisches strukturelles Designverfahren dargestellt. Genaue analytische elektromechanischer Modelle für die Bauelemente sind abgeleitet worden. Diese können unschätzbare Werkzeuge sein, um am Anfang der Designphase schnell einen klaren Einblick zur Verfügung zu stellen. Mittels des FEM Programms ist der durch die nicht-lineare Verspannung hervorgerufene versteifende Effekt nachgeforscht und sein Effekt auf die Verlängerung der mechanischen Durchstimmungsstrecke der Bauelemente demonstriert worden. Interessant war auch die Beobachtung, dass die normierte Relation zwischen Ablenkung und Spannung ein unveränderliches Profil hat. Die Deformation der Membranflächen der in dieser Arbeit dargestellten Bauelementformen erwies sich als ein unerwünschter, jedoch manchmal unvermeidbarer Effekt. Es zeigt sich aber, dass die Wahl der Größe der strukturellen Dimensionen den Grad der Membrandeformation im Falle der Aktuation beeinflusst. Diese Arbeit stellt ein elektromechanisches in FEMLAB implementierte quasi-3D Modell, das allgemein für die Modellierung dünner Strukturen angewendet werden kann, dar; und zwar indem man diese als 2D-Objekte betrachtet und die dritte Dimension als eine konstante Größe (z.B. die Schichtdicke) oder eine Größe, welche eine mathematische Funktion ist, annimmt. Diese Annahme verringert drastisch die Berechnungszeit sowie den erforderlichen Arbeitsspeicherbedarf. Weiter ist es für die Nachforschung des Effekts der Skalierung der durchstimmbaren Bauelemente verwendet worden. Eine neuartige Skalierungstechnik wurde abgeleitet und verwendet. Die Ergebnisse belegen, dass das daraus resultierende, skalierte Bauelement fast genau die gleiche mechanische Durchstimmung wie das unskalierte zeigt. Die Einbeziehung des Einflusses von axialen Verspannungen und Gradientenverspannungen in die Berechnungen erforderte die Änderung der Standardimplementierung des 3D Mechanikberechnungsmodus, der mit der benutzten FEM Software geliefert wurde. Die Ergebnisse dieser Studie zeigen einen großen Einfluss der Verspannung auf die Durchstimmungseigenschaften der untersuchten Bauelemente. Ferner stimmten die Ergebnisse der theoretischen Modellrechnung mit den experimentellen Resultaten sehr gut überein.

Molecular effects on the cross section for pair production and their importance in the evaluation of the total photonuclear cross section of {^16}O in the {\delta-resonance} region

The screening correction to the coherent pair-production cross section on the oxygen molecule has been calculated using self-consistent relativistic wave functions for the one-center and two-center Coulomb potentials. It is shown that the modification of the wave function due to molecular binding and the interference between contributions from the two atoms have both sizeable effects on the screening correction. The so-obtained coherent pair-production cross section which makes up the largest part of the total atomic cross section was used to evaluate the total nuclear absorption cross section from photon attenuation measurements on liquid oxygen. The result agrees with cross sections for other nuclei if A-scaling is assumed. The molecular effect on the pair cross section amounts to 15 % of the nuclear cross section in the {\delta-resonance} region.

Effects of Different Feeding Regimes on the Digestibility and Faecal Excretion of Nitrogen, Soluble Carbohydrates and Fibre Fractions in Water Buffaloes kept under Subtropical Conditions

In the course of the ‘Livestock Revolution’, extension and intensification of, among others, ruminant livestock production systems are current phenomena, with all their positive and negative side effects. Manure, one of the inevitable secondary products of livestock rearing, is a valuable source of plant nutrients and its skillful recycling to the soil-plant interface is essential for soil fertility, nutrient - and especially phosphorus - uses efficiency and the preservation or re-establishment of environmentally sustainable farming systems, for which organic farming systems are exemplarily. Against this background, the PhD research project presented here, which was embedded in the DFG-funded Research Training Group 1397 ‘Regulation of soil organic matter and nutrient turnover in organic agriculture ’ investigated possibilities to manipulate the diets of water buffalo (Bubalus bubalis L.) so as to produce manure of desired quality for organic vegetable production, without affecting the productivity of the animals used. Consisting of two major parts, the first study (chapter 2) tested the effects of diets differing in their ratios of carbon (C) to nitrogen (N) and of structural to non-structural carbohydrates on the quality of buffalo manure under subtropical conditions in Sohar, Sultanate of Oman. To this end, two trials were conducted with twelve water buffalo heifers each, using a full Latin Square design. One control and four tests diets were examined during three subsequent 7 day experimental periods preceded each by 21 days adaptation. Diets consisted of varying proportions of Rhodes grass hay, soybean meal, wheat bran, maize, dates, and a commercial concentrate to achieve a (1) high C/N and high NDF (neutral detergent fibre)/SC (soluble carbohydrate) ratio (HH), (2) low C/N and low NDF/SC ratio (LL); (3) high C/N and low NDF/SC ratio (HL) and (4) low C/N and high NDF/SC (LH) ratio. Effects of these diets, which were offered at 1.45 times maintenance requirements of metabolizable energy, and of individual diet characteristics, respectively, on the amount and quality of faeces excreted were determined and statistically analysed. The faeces produced from diets HH and LL were further tested in a companion PhD study (Mr. K. Siegfried) concerning their nutrient release in field experiments with radish and cabbage. The second study (chapter 3) focused on the effects of the above-described experimental diets on the rate of passage of feed particles through the gastrointestinal tract of four randomly chosen animals per treatment. To this end, an oral pulse dose of 683 mg fibre particles per kg live weight marked with Ytterbium (Yb; 14.5 mg Yb g-1 organic matter) was dosed at the start of the 7 day experimental period which followed 21 days of adaptation. During the first two days a sample for Yb determination was kept from each faecal excretion, during days 3 – 7 faecal samples were kept from the first morning and the first evening defecation only. Particle passage was modelled using a one-compartment age-dependent Gamma-2 model. In both studies individual feed intake and faecal excretion were quantified throughout the experimental periods and representative samples of feeds and faeces were subjected to proximate analysis following standard protocols. In the first study the organic matter (OM) intake and excretion of LL and LH buffaloes were significantly lower than of HH and HL animals, respectively. Digestibility of N was highest in LH (88%) and lowest in HH (74%). While NDF digestibility was also highest in LH (85%) it was lowest in LL (78%). Faecal N concentration was positively correlated (P≤0.001) with N intake, and was significantly higher in faeces excreted by LL than by HH animals. Concentrations of fibre and starch in faecal OM were positively affected by the respective dietary concentrations, with NDF being highest in HH (77%) and lowest in LL (63%). The faecal C/N ratio was positively related (P≤0.001) to NDF intake; C/N ratios were 12 and 7 for HH and LL (P≤0.001), while values for HL and LH were 11.5 and 10.6 (P>0.05). The results from the second study showed that dietary N concentration was positively affecting faecal N concentration (P≤0.001), while there was a negative correlation with the faecal concentration of NDF (P≤0.05) and the faecal ratios of NDF/N and C/N (P≤0.001). Particle passage through the mixing compartment was lower (P≤0.05) for HL (0.033 h-1) than for LL (0.043 h-1) animals, while values of 0.034 h-1 and 0.038 h-1 were obtained for groups LH and HH. At 55.4 h, total tract mean retention time was significantly (P≤0.05) lower in group LL that in all other groups where these values varied between 71 h (HH) and 79 h (HL); this was probably due to the high dietary N concentration of diet LL which was negatively correlated with time of first marker appearance in faeces (r= 0.84, P≤0.001), while the dietary C concentration was negatively correlated with particle passage through the mixing compartment (r= 0.57, P≤0.05). The results suggest that manure quality of river buffalo heifers can be considerably influenced by diet composition. Despite the reportedly high fibre digestion capacity of buffalo, digestive processes did not suppress the expression of diet characteristics in the faeces. This is important when aiming at producing a specific manure quality for fertilization purposes in (organic) crop cultivation. Although there was a strong correlation between the ingestion and the faecal excretion of nitrogen, the correlation between diet and faecal C/N ratio was weak. To impact on manure mineralization, the dietary NDF and N concentrations seem to be the key control points, but modulating effects are achieved by the inclusion of starch into the diet. Within the boundaries defined by the animals’ metabolic and (re)productive requirements for energy and nutrients, diet formulation may thus take into account the abiotically and biotically determined manure turnover processes in the soil and the nutrient requirements of the crops to which the manure is applied, so as to increase nutrient use efficiency along the continuum of the feed, the animal, the soil and the crop in (organic) farming systems.

Agri-environmental evaluation of traditional and alternative corn production systems in Chiapas, Mexico

This study evaluates the effects of environmental variables on traditional and alternative agroecosystems in three Ejidos (communal lands) in the Chiapas rainforest in Mexico. The tests occurred within two seasonal agricultural cycles. In spring-summer, experiments were performed with the traditional slash, fell and burn (S-F-B) system, no-burn systems and rotating systems with Mucuna deeringiana Bort., and in the autumn-winter agricultural cycle, three no-burn systems were compared to evaluate the effect of alternative sowing with corn (no-burn and topological modification of sowing). The results show a high floristic diversity in the study area (S_S = 4 - 23%), with no significant differences among the systems evaluated. In the first cycle, the analysis of the agronomical variables of the corn indicated better properties in the fallowing systems, with an average yield of 1950 kg ha^‑1, but there was variation related to the number of years left fallow. In the second cycle, the yields were positive for the alternative technology (average yield 3100 kg ha^‑1). The traditional S-F-B systems had reduced pests and increased organic matter and soil phosphorous content. These results are the consequence of fallow periods and adaptation to the environment; thus, this practice in the Chiapas rainforest constitutes an ethnocultural reality, which is unlikely to change in the near future if the agrosystems are managed based on historical principles.

Squeezed thermal phonons precurse nonthermal melting of silicon as a function of fluence

A femtosecond-laser pulse can induce ultrafast nonthermal melting of various materials along pathways that are inaccessible under thermodynamic conditions, but it is not known whether there is any structural modification at fluences just below the melting threshold. Here, we show for silicon that in this regime the room-temperature phonons become thermally squeezed, which is a process that has not been reported before in this material. We find that the origin of this effect is the sudden femtosecond-laser-induced softening of interatomic bonds, which can also be described in terms of a modification of the potential energy surface. We further find in ab initio molecular-dynamics simulations on laser-excited potential energy surfaces that the atoms move in the same directions during the first stages of nonthermal melting and thermal phonon squeezing. Our results demonstrate how femtosecond-laser-induced coherent fluctuations precurse complete atomic disordering as a function of fluence. The common underlying bond-softening mechanism indicates that this relation between thermal squeezing and nonthermal melting is not material specific.

Asymptotic model for shape resonance control of diatomics by intense non-resonant light: universality in the single-channel approximation

Non-resonant light interacting with diatomics via the polarizability anisotropy couples different rotational states and may lead to strong hybridization of the motion. The modification of shape resonances and low-energy scattering states due to this interaction can be fully captured by an asymptotic model, based on the long-range properties of the scattering (Crubellier et al 2015 New J. Phys. 17 045020). Remarkably, the properties of the field-dressed shape resonances in this asymptotic multi-channel description are found to be approximately linear in the field intensity up to fairly large intensity. This suggests a perturbative single-channel approach to be sufficient to study the control of such resonances by the non-resonant field. The multi-channel results furthermore indicate the dependence on field intensity to present, at least approximately, universal characteristics. Here we combine the nodal line technique to solve the asymptotic Schrödinger equation with perturbation theory. Comparing our single channel results to those obtained with the full interaction potential, we find nodal lines depending only on the field-free scattering length of the diatom to yield an approximate but universal description of the field-dressed molecule, confirming universal behavior.