Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1

The tail tape measure protein (TMP) of tailed bacteriophages (also called phages) dictates the tail length and facilitates DNA transit to the cell cytoplasm during infection. Here, a thorough mutational analysis of the TMP from lactococcal phage TP901-1 (TMPTP901-1) was undertaken. We generated 56 mutants aimed at defining TMPTP901-1 domains that are essential for tail assembly and successful infection. Through analysis of the derived mutants, we determined that TP901-1 infectivity requires the N-terminal 154 aa residues, the C-terminal 60 residues and the first predicted hydrophobic region of TMPTP901-1 as a minimum. Furthermore, the role of TMPTP901-1 in tail length determination was visualized by electron microscopic imaging of TMP-deletion mutants. The inverse linear correlation between the extent of TMPTP901-1-encoding gene deletions and tail length of the corresponding virion provides an estimate of TMPTP901-1 regions interacting with the connector or involved in initiator complex formation. This study represents the most thorough characterisation of a TMP from a Gram-positive host-infecting phage and provides essential advances to understanding its role in virion assembly, morphology and infection.

First-Principles Calculations of the Electronic and Structural Properties of GaSb

In this paper, we carried out first-principles calculations in order to investigate the structural and electronic properties of the binary compound gallium antimonide (GaSb). This theoretical study was carried out using the Density Functional Theory within the plane-wave pseudopotential method. The effects ofexchange and correlation (XC) were treated using the functional Local Density Approximation (LDA), generalized gradient approximation (GGA): Perdew–Burke–Ernzerhof (PBE), Perdew-Burke-Ernzerhof revised for solids (PBEsol), Perdew-Wang91 (PW91), revised Perdew–Burke–Ernzerhof (rPBE), Armiento–Mattson 2005 (AM05) and meta-generalized gradient approximation (meta-GGA): Tao–Perdew– Staroverov–Scuseria (TPSS) and revised Tao–Perdew–Staroverov–Scuseria (RTPSS) and modified Becke-Johnson (MBJ). We calculated the densities of state (DOS) and band structure with different XC potentials identified and compared them with the theoretical and experimental results reported in the literature. It was discovered that functional: LDA, PBEsol, AM05 and RTPSS provide the best results to calculate the lattice parameters (a) and bulk modulus (B0); while for the cohesive energy (Ecoh), functional: AM05, RTPSS and PW91 are closer to the values obtained experimentally. The MBJ, Rtpss and AM05 values found for the band gap energy is slightly underestimated with those values reported experimentally.

Adaptive strategies of two Portuguese grapevines varieties (Aragonês. syn. Tempranillo and Trincadeira) face drought: physiological and structural responses.

At Mediterranean regions and particularly in southern Portugal, it is imperative to identify grape varieties more adapted to warm and dry climates in order to overcome future climatic changes. Two Vitis vinifera genotypes, Aragonez (syn. Tempranillo) and Trincadeira, were selected to assess their physiological responses to soil water stress. Vines were subjected to four irrigation regimes: irrigated during all phenological cycle, non-irrigated during all phenological cycle, non irrigated until veraison, irrigated after veraison. Predawn leaf water potential was much higher in Trincadeira than Aragonez in non- irrigated plants. This result is in accordance with its higher stomatal control efficiency in this variety (Trincadeira). Photosynthetic capacity (Amax at saturating light intensity) decreased due to stomatal and biochemical limitations under water stress. However, recovery capacity of leaf water status after irrigation was faster in Trincadeira. Yield and yield x Brix increased when irrigation occurred after veraison, particularly in Trincadeira. These results show that Trincadeira presents a drought adaptation than Aragonez. Ratio of variable to maximum fluorescence Fv/Fm and total leaf chlorophyll related with leaf water potential for both species. Reflectance Normalized Difference Vegetation Index (NDVI705), Red Edge Inflexion Point Index and Photochemical Reflectance Index were related with irrigation treatment. Relative water content and specific leaf area were similar between varieties. In conclusion, we suggested that there is variation among the genotypes and the main physiological parameters for variety selection, for drought, were leaf water potential, stomatal conductance and reflectance indexes.

Inversion of ambient seismic noise HVSR to evaluate velocity and structural models of the Lower Tagus Basin, Portugal

During its history, several significant earthquakes have shaken the Lower Tagus Valley (Portugal). These earthquakes were destructive; some strong earthquakes were produced by large ruptures in offshore structures located southwest of the Portuguese coastline, and other moderate earthquakes were produced by local faults. In recent years, several studies have successfully obtained strong-ground motion syntheses for the Lower Tagus Valley using the finite difference method. To confirm the velocity model of this sedimentary basin obtained from geophysical and geological data, we analysed the ambient seismic noise measurements by applying the horizontal to vertical spectral ratio (HVSR) method. This study reveals the dependence of the frequency and amplitude of the low-frequency (HVSR) peaks (0.2–2 Hz) on the sediment thickness. We have obtained the depth of the Cenozoic basement along a profile transversal to the basin by the inversion of these ratios, imposing constraints from seismic reflection, boreholes, seismic sounding and gravimetric and magnetic potentials. This technique enables us to improve the existing three-dimensional model of the Lower Tagus Valley structure. The improved model will be decisive for the improvement of strong motion predictions in the earthquake hazard analysis of this highly populated basin. The methodology discussed can be applied to any other sedimentary basin.

Forage dry mass accumulation and structural characteristics of Piatã grass in silvopastoral systems in the Brazilian savannah

2016

Agronomic, morphogenic and structural characteristics of Marandu grass in silvopastoral systems composed of babassu palm and grass monoculture.

This study evaluated the agronomic, morphogenic and structural characteristics of palisadegrass (Urochloa brizantha) in silvopastoral systems (SSP?s) composed of babassu palms (Attalea speciosa) and grass monoculture in the Pre-Amazon region of the state of Maranhão, Brazil. The study followed a completely randomized design, with the arrangement in split plots with six replicates for the evaluation of agronomic characteristics and 30 repetitions for the morphogenic and structural characteristics. The plots were divided into pasture environments with different palm densities (monoculture, 80, 131, 160 palms.ha-¹), and the subplots were divided into the different seasons (rainy and dry).

Numerical modelling and structural optimization of multifunctional maritime structures aimed to protect harbours and produce energy

The main objective of this PhD thesis is to optimize a specific multifunctional maritime structure for harbour protection and energy production, named Overtopping Breakwater for Energy Conversion (OBREC), developed by the team of the University of Campania. This device is provided with a sloping plate followed by a unique reservoir, which is linked with the machine room (where the energy conversion occurs) by means of a pipe passing through the crown wall, provided with a parapet on top of it. Therefore, the potential energy of the overtopping waves, collected inside the reservoir located above the still water level, is then converted by means of low – head turbines. In order to improve the understanding of the wave – structure interactions with OBREC, several methodologies have been used and combined together: i. analysis of recent experimental campaigns on wave overtopping discharges and pressures at the crown wall on small – scale OBREC cross sections, carried out in other laboratories by the team of the University of Campania; ii. new experiments on cross sections similar to the OBREC device, planned and carried out in the hydraulic lab at the University of Bologna in the framework of this PhD work; iii. numerical modelling with a 1 – phase incompressible fluid model IH – 2VOF, developed by the University of Cantabria, and with a 2 – phase incompressible fluid model OpenFOAM, both available from the literature; iv. numerical modelling with a new 2 – phase compressible fluid model developed in the OpenFOAM environment within this PhD work; v. analysis of the data gained from the monitoring of the OBREC prototype installation.

Subsidence history, thermal maturity, and structural inversion of the Greater Caucasus-Kura-Adjara-Trialeti basin system of central-eastern Georgia

This study aims at defining the tectonic evolution of a portion of the Caucasian region, in Georgia, which experienced a complex pattern of deformation events throughout Mesozoic and Cenozoic times. An integrated approach was applied to unravel the thermo-tectonic history of three inverted sedimentary basins from burial to exhumation. Additionally, this dissertation provides examples of structural inversion of sedimentary basins in response to far-field transmission of compressional stresses away from collision zones, contributing to elucidate the dynamics of stress partitioning during continental collisions. The Adjara-Trialeti fold-and-thrust belt in south-western Georgia results from the structural inversion of a Middle Eocene continental back-arc rift basin opened as a consequence of the Northern Neotethys slab rollback. This study quantitatively defines the subsidence and exhumation history of the Adjara-Trialeti basin, constraining its Middle Miocene inception of structural inversion. The western Kura Basin is a flexural foreland basin trapped between the Lesser Caucasus to the south and the Greater Caucasus to the north. This study constrains successive and competing episodes of flexural subsidence during Oligocene-Miocene times, followed by partial inversion through thick- and thin-skinned tectonics in response to continued convergence between the adjacent, oppositely verging orogenic belts. The Greater Caucasus results from the structural inversion of a Jurassic continental back-arc basin, but the timing of its growth is still debated. An across-strike transect in its southern central domain was studied, indicating that this sector of the Greater Caucasus experienced two phases of structural inversion during Late Cretaceous-Paleocene and Late Miocene times. Overall, the dataset presented in this dissertation points to a complex and episodic history of incremental deformation, characterised by successive phases of extensional and compressional tectonics which developed in response to sequential terrane accretion at the southwestern margin of Eurasia since Late Cretaceous times, eventually determining the current configuration of the Arabia-Eurasia collision zone.

Protein-based nanomaterials as protein heterogeneous nucleants and structural studies on enzymes from two photosynthetic organisms

Proteins, the most essential biological macromolecules, are involved in nearly every aspect of life. The elucidation of their three-dimensional structures through X-ray analysis has significantly contributed to our understanding of fundamental mechanisms in life processes. However, the obstacle of obtaining high-resolution protein crystals remains significant. Thus, searching for materials that can effectively induce nucleation of crystals is a promising and active field. This thesis work characterizes and prepares albumin nanoparticles as heterogeneous nucleants for protein crystallization. These stable Bovine Serum Albumin nanoparticles were synthesized via the desolvation method, purified efficiently, and characterized in terms of dimension, morphology, and secondary structure. The ability of BSA-NPs to induce macromolecule nucleation was tested on three model proteins, exhibiting significant results, with larger NPs inducing more nucleation. The second part of this work focuses on the structural study, mainly through X-ray crystallography, of five chloroplast and cytosolic enzymes involved in the fundamental cellular processes of two photosynthetic organisms, Chlamydomonas reinhardtii and Arabidopsis thaliana. The structures of three enzymes involved in the Calvin-Benson-Bassham Cycle, phosphoribulokinase, troseposphatisomerase, and ribulosiophosphate epimerase from Chlamydomonas reinhardtii, were solved to investigate their catalytic and regulatory mechanisms. Additionally, the structure of nitrosylated-CrTPI made it possible to identify Cys14 as a target for nitrosylation, and the crystallographic structure of CrRPE was solved for the first time, providing insights into its catalytic and regulatory properties. Finally, the structure of S-nitrosoglutathione reductase, AtGSNOR, was compared with that of AtADH1, revealing differences in their catalytic sites. Overall, seven crystallographic structures, including partially oxidized CrPRK, CrPRK/ATP, CrPRK/ADP/Ru5P, CrTPI-nitrosylated, apo-CrRPE, apo-AtGSNOR, and AtADH1-NADH, were solved and are yet to be deposited in the PDB.

Cardiac functional and structural abnormalities in a mouse model of CDKL5 deficiency disorder

CDKL5 (cyclin-dependent kinase-like 5) deficiency disorder (CDD) is a rare and severe neurodevelopmental disease that mostly affects girls who are heterozygous for mutations in the X-linked CDKL5 gene. The lack of CDKL5 protein expression or function leads to the appearance of numerous clinical features, including early-onset seizures, marked hypotonia, autistic features, and severe neurodevelopmental impairment. Mouse models of CDD, Cdkl5 KO mice, exhibit several behavioral phenotypes that mimic CDD features, such as impaired learning and memory, social interaction, and motor coordination. CDD symptomatology, along with the high CDKL5 expression levels in the brain, underscores the critical role that CDKL5 plays in proper brain development and function. Nevertheless, the improvement of the clinical overview of CDD in the past few years has defined a more detailed phenotypic spectrum; this includes very common alterations in peripheral organ and tissue function, such as gastrointestinal problems, irregular breathing, hypotonia, and scoliosis, suggesting that CDKL5 deficiency compromises not only CNS function but also that of other organs/tissues. Here we report, for the first time, that a mouse model of CDD, the heterozygous Cdkl5 KO (Cdkl5 +/-) female mouse, exhibits cardiac functional and structural abnormalities. The mice also showed QTc prolongation and increased heart rate. These changes correlate with a marked decrease in parasympathetic activity to the heart and in the expression of the Scn5a and Hcn4 voltage-gated channels. Moreover, the Cdkl5 +/- heart shows typical signs of heart aging, including increased fibrosis, mitochondrial dysfunctions, and increased ROS production. Overall, our study not only contributes to the understanding of the role of CDKL5 in heart structure/function but also documents a novel preclinical phenotype for future therapeutic investigation.

Study of charge, spin, and structural orderings in quantum materials using nuclei and muons as local probes

Quantum Materials are many body systems displaying emergent phenomena caused by quantum collective behaviour, such as superconductivity, charge density wave, fractional hall effect, and exotic magnetism. Among quantum materials, two families have recently attracted attention: kagome metals and Kitaev materials. Kagome metals have a unique crystal structure made up of triangular lattice layers that are used to form the kagome layer. Due to superconductivity, magnetism, and charge ordering states such as the Charge Density Wave (CDW), unexpected physical phenomena such as the massive Anomalous Hall Effect (AHE) and possible Majorana fermions develop in these materials. Kitaev materials are a type of quantum material with a unique spin model named after Alexei Kitaev. They include fractional fluctuations of Majorana fermions and non-topological abelian anyons, both of which might be used in quantum computing. Furthermore, they provide a realistic framework for the development of quantum spin liquid (QSL), in which quantum fluctuations produce long-range entanglements between electronic states despite the lack of classical magnetic ordering. In my research, I performed several nuclear magnetic resonance (NMR), nuclear quadrupole resonance (NQR), and muon spin spectroscopy (µSR) experiments to explain and unravel novel phases of matter within these unusual families of materials. NMR has been found to be an excellent tool for studying these materials’ local electronic structures and magnetic properties. I could use NMR to determine, for the first time, the structure of a novel kagome superconductor, RbV3Sb5, below the CDW transition, and to highlight the role of chemical doping in the CDW phase of AV3Sb5 superconductors. µSR has been used to investigate the effect of doping on kagome material samples in order to study the presence and behaviour of an anomalous phase developing at low temperatures and possibly related to time-reversal symmetry breaking.

Novel management to enhance spider biodiversity in existing grass buffer strips

Grass buffer strips have been widely sown to mitigate against intensive agricultural management practices that have negatively impacted on invertebrate and plant biodiversity in arable farming systems. Typically, such strips are floristically species poor and are dominated by grasses. In the present study, we developed management practices to enhance the floristic and structural diversity of these existing strips for the benefit of spiders, a key provider of natural pest control in crops. Across three UK arable farms, we investigated the benefits of: (i) scarification to create germination niches into which wildflower seeds were sown and (ii) the effect of graminicide applications to suppress grass dominance. Spiders were sampled twice per year (July and September) during 2008 and 2009. The combination of scarification with wildflower seeds, as well as graminicide, resulted in the greatest wildflower cover and lowest grass cover, with a general trend of increased abundance of adult and juvenile spiders. The abundance of Pachygnatha degeeri, Bathyphantes gracilis and juvenile wolf spiders of the genus Pardosa was positively correlated with wildflower cover, probably reflecting increased prey availability. Sward structure was negatively correlated with Erigone atra, Oedothorax fuscus and juvenile Pardosa abundance. Management that utilizes existing commonly adopted agri-environment options, such as grass buffer strips, represents a potentially important conservation tool for increasing the quantity and quality of invertebrate habitats. This can maximize opportunities for the provision of multiple ecosystem services, including pest regulation by predators such as spiders. These management practices have the potential to be incorporated into existing U.K. and European agri-environment schemes.

Análise fitoecológica do manguezal e ocupação das margens do estuário hipersalino apodi/mossoró (rn brasil) a biotecnologia vegetal como alternativa para a cotonicultura

The mangrove is a coastal ecosystem of the big ecological importance, showing high fragility front by natural process and the human interventions in the coastal zone. This research has objective to analyses the relation between mangrove species distribution and geochemical parameters variation of the water and soil in Apodi/Mossoro estuary, located in the Rio Grande do Norte state north coastline. The results were obtained from floristic and structural analysis of the vegetation and Quick Bird satellite images interpretation (collected in 2006 year), manipulated with ENVI 4.3 and ArcGIS 9.2 software s. This estuary was characterized by to presents a gradient of the salinity around 40 kilometers extension, finding amount between 50 and 90 g/l-1. Will be identified the formation of the mix vegetation formation in the estuary mount, where the water salinity no show express wide variation on seawater (36 g/l-1), finding species: Rhizophora mangle L., Laguncularia racemosa (L.) C. F. Gaertn, Avicennia schaueriana Stap. & Leechman e Avicennia germinans L. Along of the estuary, have a streak formation of the vegetation composed by Avicennia spp. and L. racemosa. In high estuary, where the salinities value stay above 60 g/l-1, only A. germinans predominate in dwarf form. In this sense, the salinity is as a limiting factor of stress on the mangrove vegetation as it enters the estuary, this parameter should be taken into account when drawing up management plans and environmental restoration in the estuary in question

Composição florística e estrutura da comunidade arbórea na transição da Floresta Ombrófila Densa das Terras Baixas - Floresta Ombrófila Densa Submontana do Núcleo Picinguaba/PESM, Ubatuba, sudeste do Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estrutura de um trecho de floresta Amazônica na bacia do alto rio Xingu

Este estudo apresenta a estrutura de florestas em Gaúcha do Norte-MT (13° 10'S e 53° 15' O), na borda sul-amazônica. Para o levantamento fitossociológico, três áreas amostrais de 1ha foram subdivididas em 50 parcelas de 10x20m, nas quais foram amostrados todos os indivíduos com perímetro à altura do peito (PAP) >15 cm. Para verificar a similaridade estrutural entre as áreas utilizou-se a Análise de Correspondência. As espécies indicadoras dos ambientes de interflúvio e das áreas sujeitas à inundação foram obtidas através do TWINSPAN e de um sistema de pesos. Concluiu-se que as florestas presentes na bacia do rio Pacuneiro pertencem à mesma unidade fitogeográfica, mas com subtipos florísticos e estruturais de acordo com a posição no relevo, a proximidade dos cursos d'água e o estrato analisado, apresentando predominância de algumas espécies, ou até mesmo possíveis endemismos, em determinados trechos ou estratos. A formação apresentou baixa diversidade alfa (2,91 a 3,50) e beta (3,62 a 3,86), o que não é comum em florestas amazônicas. Várias hipóteses podem explicar essa baixa diversidade, entre elas a baixa precipitação e a alta sazonalidade, o ambiente físico regional aparentemente homogêneo e favorável às espécies competidoras, ou os eventos históricos, relacionados à possível exploração por tribos indígenas ou à recente expansão dessas florestas sobre as áreas savânicas.