Theoretical Study of the Absorption Spectra of Photosynthetic Pigments

The first stage of the photosynthetic process is the extraordinary efficiency of sunlight absorption in the visible region [1]. This region corresponds to the maximum of the spectral radiance of the solar emission. The efficient absorption of visible light is one of the most important characteristics of photosynthetic pigments. In chlorophylls, for example, the absorptions are seen as a strong absorption in the region 400-450 nm in connection with other absorptions with small intensities in the region of 500-600 nm. This work aims at understanding the essential features of the absorption spectrum of photosynthetic pigments, in line with several theoretical studies in the literature [2, 3]. The absorption spectra were calculated for H2-Porphyrin, Mg-Porphyrin, and Zn-Porphyrin, and for H2-Phthalocyanine and Mg-Phthalocyanine with and without the four peripheral eugenol substituents. The geometries were optimized using the B3LYP/6-31+G(d) theoretical model. For the calculation of the absorption spectra different TD-DFT calculations were performed (B3LYP, CAM-B3LYP, O3LYP, M06-2X and BP86) along with CIS (D). For the spectra the basis set 6-311++G (d, p) was used for porphyrins and 6-31+G (d) was used for the other systems. At this stage the solvent effects were considered using the simplified continuum model (PCM). First a comparison between the results using the different methods was made. For the porphyrins the best results compared to experiment (both in position and intensities) are obtained with M06-2X and CIS (D). We also analyze the compatibility of the four-orbital model of Gouterman [4] that states that transitions could be well described by the HOMO-1, HOMO, LUMO, and LUMO+1 molecular orbitals. Our results for H2-Porphyrin shows an agreement with other theoretical results and experimental data [5]. For the phthalocyanines (including the four peripheral eugenol substituents) the results are also in good agreement compared with the experimental results given in ref [6]. Finally, the results show that the inclusion of solvent eÆects gives corrections for the spectral shift in the correct direction but numerically small. References [1] R.E. Blankenship; “Molecular Mechanisms of Photosynthesis", Blackwell Science (2002). [2] P. Jaramillo, K. Coutinho, B.J.C. Cabral and S. Canuto; Chem. Phys. Lett., 516, 250(2011). [3] L. Petit, A. Quartarolo, C. Adamo and N. Russo; J. Phys. Chem. B, 110, 2398(2006). [4] M. J. Gouterman; Mol. Spectr., 6, 138(1961). [5] M. Palummo, C. Hogan, F. Sottile, P. Bagal∂a and A. Rubio; J. Chem. Phys., 131, 084102(2009). [6] E. Agar, S. Sasmaz and A. Agar; Turk. J. Chem., 23, 131(1999).

Evolution of signal form

Visual signals, used for communication both within and between species, vary immensely in the forms that they take. How is it that all this splendour has evolved in nature? Since it is the receiver’s preferences that cause selective pressures on signals, elucidating the mechanism behind the response of the signal receiver is vital to gain a closer understanding of the evolutionary process. In my thesis I have therefore investigated how receivers, represented by chickens, Gallus gallus domesticus, respond to different stimuli displayed on a peck-sensitive computer screen. According to the receiver bias hypothesis, animals and humans often express biases when responding to certain stimuli. These biases develop as by-products of how the recognition mechanism categorises and discriminates between stimuli. Since biases are generated from general stimulus processing mechanisms, they occur irrespective of species and type of signal, and it is often possible to predict the direction and intensity of the biases. One of the results from the experiments in my thesis demonstrates that similar experience in different species may generate similar biases. By giving chickens at least some of the experience of human faces as humans presumably have, the chickens subsequently expressed preferences for the same faces as a group of human subjects. Another kind of experience generated a bias for symmetry. This bias developed in the context of training chickens to recognise two mirror images of an asymmetrical stimulus. Untrained chickens and chickens trained on only one of the mirror images expressed no symmetry preferences. The bias produced by the training regime was for a specific symmetrical stimulus which had a strong resemblance to the familiar asymmetrical exemplar, rather than a general preference for symmetry. A further kind of experience, training chickens to respond to some stimuli but not to others, generated a receiver bias for exaggerated stimuli, whereas chickens trained on reversed stimuli developed a bias for less exaggerated stimuli. To investigate the potential of this bias to drive the evolution of signals towards exaggerated forms, a simplified evolutionary process was mimicked. The stimuli variants rejected by the chickens were eliminated, whereas the selected forms were kept and evolved prior to the subsequent display. As a result, signals evolved into exaggerated forms in all tested stimulus dimensions: length, intensity and area, despite the inclusion of a cost to the sender for using increasingly exaggerated signals. The bias was especially strong and persistent for stimuli varying along the intensity dimension where it remained despite extensive training. All the results in my thesis may be predicted by the receiver bias hypothesis. This implies that biases, developed due to stimuli experience, may be significant mechanisms driving the evolution of signal form.

Molecular characterization of the human gut microbiota: the effect of aging

Age-related physiological changes in the gastrointestinal tract, as well as modification in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota. The study presented here is focused on the application and comparison of two different microarray approaches for the characterization of the human gut microbiota, the HITChip and the HTF-Microb.Array, with particular attention to the effects of the aging process on the composition of this ecosystem. By using the Human Intestinal Tract Chip (HITChip), recently developed at the Wageningen University, The Netherland, we explored the age-related changes of gut microbiota during the whole adult lifespan, from young adults, through elderly to centenarians. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment of facultative anaerobes. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammation status, also known as inflamm-aging, as determined by a range of peripheral blood inflammatory markers. In parallel, we overtook the development of our own phylogenetic microarray with a lower number of targets, aiming the description of the human gut microbiota structure at high taxonomic level. The resulting chip was called High Taxonomic level Fingerprinting Microbiota Array (HTF-Microb.Array), and was based on the Ligase Detection Reaction (LDR) technology, which allowed us to develop a fast and sensitive tool for the fingerprint of the human gut microbiota in terms of presence/absence of the principal groups. The validation on artificial DNA mixes, as well as the pilot study involving eight healthy young adults, demonstrated that the HTF-Microb.Array can be used to successfully characterize the human gut microbiota, allowing us to obtain results which are in approximate accordance with the most recent characterizations. Conversely, the evaluation of the relative abundance of the target groups on the bases of the relative fluorescence intensity probes response still has some hindrances, as demonstrated by comparing the HTF.Microb.Array and HITChip high taxonomic level fingerprints of the same centenarians.

Study of the components of quality in SO2-free wines obtained by innovative vinification protocols. Evaluation of the pre-fermentative addition of lysozyme and oenological tannins.

The research performed during the PhD candidature was intended to evaluate the quality of white wines, as a function of the reduction in SO2 use during the first steps of the winemaking process. In order to investigate the mechanism and intensity of interactions occurring between lysozyme and the principal macro-components of musts and wines, a series of experiments on model wine solutions were undertaken, focusing attention on the polyphenols, SO2, oenological tannins, pectines, ethanol, and sugar components. In the second part of this research program, a series of conventional sulphite added vinifications were compared to vinifications in which sulphur dioxide was replaced by lysozyme and consequently define potential winemaking protocols suitable for the production of SO2-free wines. To reach the final goal, the technological performance of two selected yeast strains with a low aptitude to produce SO2 during fermentation were also evaluated. The data obtained suggested that the addition of lysozyme and oenological tannins during the alcoholic fermentation could represent a promising alternative to the use of sulphur dioxide and a reliable starting point for the production of SO2-free wines. The different vinification protocols studied influenced the composition of the volatile profile in wines at the end of the alcoholic fermentation, especially with regards to alcohols and ethyl esters also a consequence of the yeast’s response to the presence or absence of sulphites during fermentation, contributing in different ways to the sensory profiles of wines. In fact, the aminoacids analysis showed that lysozyme can affect the consumption of nitrogen as a function of the yeast strain used in fermentation. During the bottle storage, the evolution of volatile compounds is affected by the presence of SO2 and oenological tannins, confirming their positive role in scaveging oxygen and maintaining the amounts of esters over certain levels, avoiding a decline in the wine’s quality. Even though a natural decrease was found on phenolic profiles due to oxidation effects caused by the presence of oxygen dissolved in the medium during the storage period, the presence of SO2 together with tannins contrasted the decay of phenolic content at the end of the fermentation. Tannins also showed a central role in preserving the polyphenolic profile of wines during the storage period, confirming their antioxidant property, acting as reductants. Our study focused on the fundamental chemistry relevant to the oxidative phenolic spoilage of white wines has demonstrated the suitability of glutathione to inhibit the production of yellow xanthylium cation pigments generated from flavanols and glyoxylic acid at the concentration that it typically exists in wine. The ability of glutathione to bind glyoxylic acid rather than acetaldehyde may enable glutathione to be used as a ‘switch’ for glyoxylic acid-induced polymerisation mechanisms, as opposed to the equivalent acetaldehyde polymerisation, in processes such as microoxidation. Further research is required to assess the ability of glutathione to prevent xanthylium cation production during the in-situ production of glyoxylic acid and in the presence of sulphur dioxide.

Mode coupling for precise measurements of the electronic g-factor of hydrogen-like ions in Penning traps

The g-factor is a constant which connects the magnetic moment $vec{mu}$ of a charged particle, of charge q and mass m, with its angular momentum $vec{J}$. Thus, the magnetic moment can be writen $ vec{mu}_J=g_Jfrac{q}{2m}vec{J}$. The g-factor for a free particle of spin s=1/2 should take the value g=2. But due to quantum electro-dynamical effects it deviates from this value by a small amount, the so called g-factor anomaly $a_e$, which is of the order of $10^{-3}$ for the free electron. This deviation is even bigger if the electron is exposed to high electric fields. Therefore highly charged ions, where electric field strength gets values on the order of $10^{13}-10^{16}$V/cm at the position of the bound electron, are an interesting field of investigations to test QED-calculations. In previous experiments [H"aff00,Ver04] using a single hydrogen-like ion confined in a Penning trap an accuracy of few parts in $10^{-9}$ was obtained. In the present work a new method for precise measurement of magnetic the electronic g-factor of hydrogen-like ions is discussed. Due to the unavoidable magnetic field inhomogeneity in a Penning trap, a very important contribution to the systematic uncertainty in the previous measurements arose from the elevated energy of the ion required for the measurement of its motional frequencies. Then it was necessary to extrapolate the result to vanishing energies. In the new method the energy in the cyclotron degree of freedom is reduced to the minimum attainable energy. This method consist in measuring the reduced cyclotron frequency $nu_{+}$ indirectly by coupling the axial to the reduced cyclotron motion by irradiation of the radio frequency $nu_{coup}=nu_{+}-nu_{ax}+delta$ where $delta$ is, in principle, an unknown detuning that can be obtained from the knowledge of the coupling process. Then the only unknown parameter is the desired value of $nu_+$. As a test, a measurement with, for simplicity, artificially increased axial energy was performed yielding the result $g_{exp}=2.000~047~020~8(24)(44)$. This is in perfect agreement with both the theoretical result $g_{theo}=2.000~047~020~2(6)$ and the previous experimental result $g_{exp1}=2.000~047~025~4(15)(44).$ In the experimental results the second error-bar is due to the uncertainty in the accepted value for the electron's mass. Thus, with the new method a higher accuracy in the g-factor could lead by comparison to the theoretical value to an improved value of the electron's mass. [H"af00] H. H"affner et al., Phys. Rev. Lett. 85 (2000) 5308 [Ver04] J. Verd'u et al., Phys. Rev. Lett. 92 (2004) 093002-1

The pre-alpine evolution of the basement of the Pelagonian Zone and the Vardar Zone, Greece

The Pelagonian Zone and the Vardar Zone in Greece represent the western part of the Hellenide hinterland (Internal Hellenides). While the Pelagonian Zone comprises predominantly crystalline basement and sedimentary cover rocks, the Vardar Zone has long been regarded as an ophiolite-decorated suture zone separating the Pelagonian Zone from the Serbo-Macedonian Massif to the east. Felsic basement rocks from both areas, with the main focus put on the Pelagonian Zone, were dated in order to identify the major crust-forming episodes and to improve the understanding of the evolutionary history of the region. The interpretation of the single-zircon geochronology results was aided by geochemical investigations. The majority of the basement rocks from the Pelagonian Zone yielded Permo-Carboniferous intrusion ages around 300 Ma, underlining the importance of this crust-forming event for the Internal Hellenides of Greece. Geochemically these basement rocks are classified as subduction-related granitoids, which formed in an active continental margin setting. An important result was the identification of a Precambrian crustal unit within the crystalline basement of the Pelagonian Zone. Orthogneisses from the NW Pelagonian Zone yielded Neoproterozoic ages of c. 700 Ma and are so far the oldest known rocks in Greece. These basement rocks, which are also similar to active margin granitoids, were interpreted as remnants of a terrane, the Florina Terrane, which can be correlated to a Pan-African or Cadomian arc. Since the gneisses contain inherited zircons of Middle to Late Proterozoic ages, the original location of the Florina Terrane was probably at the northwestern margin of Gondwana. In the Vardar Zone an important phase of Upper Jurassic felsic magmatism is documented by igneous formation ages ranging from 155 to 164 Ma. The chemical and isotopic composition of these rocks is also in accord with their formation in a volcanic-arc setting at an active continental margin. Older continental material incorporated in the Vardar Zone is documented by 319-Ma-old gneisses and by inherited zircons of mainly Middle Palaeozoic ages. The prevalence of subduction-related igneous rocks indicates that arc formation and accretion orogeny were the most important processes during the evolution of this part of the Internal Hellenides. The geochronological results demonstrate that most of the Pelagonian Zone and the Vardar Zone crystalline basement formed during distinct pre-Alpine episodes at c. 700, 300 and 160 Ma with a predominance of the Permo-Carboniferous magmatic phase.

Spatial and temporal variability and ecological processes in the epibenthic assemblages of the northern Adriatic Sea

Several coralligenous reefs occur in the soft bottoms of the northern Adriatic continental shelf. Mediterranean coralligenous habitats are characterised by high species diversity and are intrinsically valuable for their biological diversity and for the ecological processes they support. The conservation and management of these habitats require quantifying spatial and temporal variability of their benthic assemblages. This PhD thesis aims to give a relevant contribution to the knowledge of the structure and dynamics of the epibenthic assemblages on the coralligenous subtidal reefs occurring in the northern Adriatic Sea. The epibenthic assemblages showed a spatial variation larger compared to temporal changes, with a temporal persistence of reef-forming organisms. Assemblages spatial heterogeneity has been related to morphological features and geographical location of the reefs, together with variation in the hydrological conditions. Manipulative experiments help to understand the ecological processes structuring the benthic assemblages and maintaining their diversity. In this regards a short and long term experiment on colonization patterns of artificial substrata over a 3-year period has been performed in three reefs, corresponding to the three main types of assemblages detected in the previous study. The first colonisers, largely depending by the different larval supply, played a key role in determining the heterogeneity of the assemblages in the early stage of colonisation. Lateral invasion, from the surrounding assemblages, was the driver in structuring the mature assemblages. These complex colonisation dynamics explained the high heterogeneity of the assemblages dwelling on the northern Adriatic biogenic reefs. The buildup of these coralligenous reefs mainly depends by the bioconstruction-erosion processes that has been analysed through a field experiment. Bioconstruction, largely due to serpulid polychaetes, prevailed on erosion processes and occurred at similar rates in all sites. Similarly, the total energy contents in the benthic communities do not differ among sites, despite being provided by different species. Therefore, we can hypothesise that both bioconstruction processes and energetic storage may be limited by the availability of resources. Finally the major contribution of the zoobenthos compared to the phytobenthos to the total energetic content of assemblages suggests that the energy flow in these benthic habitats is primarily supported by planktonic food web trough the filter feeding invertebrates.

Morphology of the nasopalatine canal and dental implant surgery: a radiographic analysis of 100 consecutive patients using limited cone-beam computed tomography

To analyze the dimensions and anatomic characteristics of the nasopalatine canal and the corresponding buccal bone plate of the alveolar process, using limited cone-beam computed tomography (CBCT) imaging.

Reporting Experiments in Homeopathic Basic Research—Description of the Checklist Development

The objective of this study was to develop a criteria catalogue serving as a guideline for authors to improve quality of reporting experiments in basic research in homeopathy. A Delphi Process was initiated including three rounds of adjusting and phrasing plus two consensus conferences. European researchers who published experimental work within the last 5 years were involved. A checklist for authors provide a catalogue with 23 criteria. The “Introduction” should focus on underlying hypotheses, the homeopathic principle investigated and state if experiments are exploratory or confirmatory. “Materials and methods” should comprise information on object of investigation, experimental setup, parameters, intervention and statistical methods. A more detailed description on the homeopathic substances, for example, manufacture, dilution method, starting point of dilution is required. A further result of the Delphi process is to raise scientists' awareness of reporting blinding, allocation, replication, quality control and system performance controls. The part “Results” should provide the exact number of treated units per setting which were included in each analysis and state missing samples and drop outs. Results presented in tables and figures are as important as appropriate measures of effect size, uncertainty and probability. “Discussion” in a report should depict more than a general interpretation of results in the context of current evidence but also limitations and an appraisal of aptitude for the chosen experimental model. Authors of homeopathic basic research publications are encouraged to apply our checklist when preparing their manuscripts. Feedback is encouraged on applicability, strength and limitations of the list to enable future revisions.

An anatomical investigation of the cervicothoracic ganglion

Anatomical variability within the autonomic nervous system has long been accepted. This study evaluated the anatomical variability of the cervicothoracic ganglion (CTG) according to its form and, in addition, provided precise measurements between the CTG and the anterior tubercle of the transverse process of the sixth cervical vertebra (C6TP), the first costovertebral articulation, and the vertebral artery. Forty-two adult cadavers were dissected, 22 male and 20 females. Five main forms of CTG were documented; spindle (31.9%), dumbbell (23.2%), truncated (21.7%), perforated (14.5%), and inverted-L (8.7%). The means for length, width, and thickness of the CTG were 18.5 mm, 8.2 mm, and 4.5 mm, respectively. The dimensions were found to be slightly larger in the males than females and on the left sides as compared to the right. The mean shortest distance between the CTGs and the vertebral artery was found to be 2.8 mm, whilst the mean shortest distances to C6TP was 25.7 mm and to the first costovertebral articulation was 1.7 mm. There is great variability in the morphology of the CTG with five common forms consistently seen. The relation to the vertebral artery may influence the form of the ganglion. Two previously undocumented forms are recorded; the truncated which describes the important juxtaposition of the CTG and the vertebral artery and the perforated which describes the piercing of the ganglion itself by the artery. The findings are considered to be of clinical importance to anesthetists, surgeons, neurosurgeons, and anatomists.

Monostotic fibrous dysplasia of the spine: report of a case involving a cervical vertebra

Monostotic fibrous dysplasia of the spine is a rare entity. Only 26 cases, of which 11 were located in the cervical spine, are to be found in the literature. We report a 56-year-old male patient with cervicobrachialgia of half year's duration. Radiographs showed a diffuse destruction of the vertebral body and the spinous process of C4. A biopsy of the spinous process confirmed histopathologically a fibrous dysplasia. Due to minor symptoms, no surgical treatment was performed or is planned unless in case of increasing pain, an acute instability or neurological symptoms.

The association of the composite IL-1 genotype with periodontitis progression and/or treatment outcomes: a systematic review

BACKGROUND: Genetically transmitted traits such as cytokine gene polymorphisms may accentuate the host inflammatory response to the bacterial challenge and influence susceptibility to periodontitis. OBJECTIVE: To systematically review the evidence of an association between the interleukin-1 (IL-1) composite genotype, i.e. presence of the allele 2 in the gene clusters IL-1A-889 and in IL-1B +3953, and periodontitis progression and/or treatment outcomes. Material and Methods: Based on the focused question, a search was conducted for longitudinal clinical trials comparing progression of periodontitis and/or treatment outcomes in IL-1 genotype-positive (carrying allele 2) and IL-1 genotype-negative (not carrying allele 2) subjects. A search in the National Library of Medicine computerized bibliographic database MEDLINE and a manual search were performed. Selection of publications, extraction of data and validity assessment were made independently by two reviewers. RESULTS: The search provided 122 titles of which 11 longitudinal publications were included. The heterogeneity of the data prevented the performance of a meta-analysis. While findings from some publications rejected a possible role of IL-1 composite genotype on progression of periodontitis after various therapies, other reported a prognostic value for disease progression of the positive IL-1 genotype status. When assessed on a multivariate risk assessment model, several publications concluded that the assessment of the IL-1 composite genotype in conjunction with other covariates (e.g. smoking and presence of specific bacteria) may provide additional information on disease progression. The small sample size of the available publications, however, requires caution in the interpretation of the results. CONCLUSION: Based on these findings, (i) there is insufficient evidence to establish if a positive IL-1 genotype status contributes to progression of periodontitis and/or treatment outcomes. Therefore, (ii) results obtained with commercially available tests should be interpreted with caution.

Resolving the tragedy of the commons: the feedback between intraspecific conflict and population density

Competition and conflict among individuals can favour exploitative strategies that undermine the common good. Theory suggests that this can lead to a tragedy of the commons and ultimately population extinction, a phenomenon known as evolutionary suicide. Here, I present a model of the evolutionary tragedy of the commons that explicitly considers the population dynamics where individuals invest in individually costly competitive traits. In the simplest form, this supports the notion that selection for high levels of conflict can cause evolutionary suicide. However, as competition comes with survival and fecundity costs, a feedback between the investment in competition and population density can act to reduce the level of conflict and prevent the population from going extinct. This suggests that the interaction between population ecology and the evolution of competition and conflict among individuals may be an important mechanism in resolving the level of competition and conflict among individuals.

Limited open reduction and internal fixation of displaced intra-articular fractures of the calcaneum

The extended lateral L-shaped approach for the treatment of displaced intra-articular fractures of the calcaneum may be complicated by wound infection, haematoma, dehiscence and injury to the sural nerve. In an effort to reduce the risk of problems with wound healing a technique was developed that combined open reduction and fixation of the joint fragments and of the anterior process with percutaneous reduction and screw fixation of the tuberosity. A group of 24 patients with unilateral isolated closed Sanders type II and III fractures was treated using this technique and compared to a similar group of 26 patients managed by the extended approach and lateral plating. The operation was significantly shorter (p < 0.001) in the first group, but more minor secondary procedures and removal of heel screws were necessary. There were no wound complications in this group, whereas four minor complications occurred in the second group. The accuracy and maintenance of reduction, and ultimate function were equivalent.

Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework

The present distribution of freshwater fish in the Alpine region has been strongly affected by colonization events occurring after the last glacial maximum (LGM), some 20,000 years ago. We use here a spatially explicit simulation framework to model and better understand their colonization dynamics in the Swiss Rhine basin. This approach is applied to the European bullhead (Cottus gobio), which is an ideal model organism to study fish past demographic processes since it has not been managed by humans. The molecular diversity of eight sampled populations is simulated and compared to observed data at six microsatellite loci under an approximate Bayesian computation framework to estimate the parameters of the colonization process. Our demographic estimates fit well with current knowledge about the biology of this species, but they suggest that the Swiss Rhine basin was colonized very recently, after the Younger Dryas some 6600 years ago. We discuss the implication of this result, as well as the strengths and limits of the spatially explicit approach coupled to the approximate Bayesian computation framework.