Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change

Ecosystem functioning in grasslands is regulated by a range of biotic and abiotic factors, and the role of microbial communities in regulating ecosystem function has been the subject of much recent scrutiny. However, there are still knowledge gaps regarding the impacts of rainfall and vegetation change upon microbial communities and the implications of these changes for ecosystem functioning. We investigated this issue using data from an experimental mesotrophic grassland study in south-east England, which had been subjected to four years of rainfall and plant functional composition manipulations. Soil respiration, nitrogen and phosphorus stocks were measured, and the abundance and community structure of soil microbes were characterised using quantitative PCR and multiplex-TRFLP analysis, respectively. Bacterial community structure was strongly related to the plant functional composition treatments, but not the rainfall treatment. However, there was a strong effect of both rainfall change and plant functional group upon bacterial abundance. There was also a weak interactive effect of the two treatments upon fungal community structure, although fungal abundance was not affected by either treatment. Next, we used a statistical approach to assess whether treatment effects on ecosystem function were regulated by the microbial community. Our results revealed that ecosystem function was influenced by the experimental treatments, but was not related to associated changes to the microbial community. Overall, these results indicate that changes in fungal and bacterial community structure and abundance play a relatively minor role in determining grassland ecosystem function responses to precipitation and plant functional composition change, and that direct effects on soil physical and chemical properties and upon plant and microbial physiology may play a more important role.

Biodiversity and Ecosystem Function in the Gulf of Maine: Pattern and Role of Zooplankton and Pelagic Nekton

This paper forms part of a broader overview of biodiversity of marine life in the Gulf of Maine area (GoMA), facilitated by the GoMA Census of Marine Life program. It synthesizes current data on species diversity of zooplankton and pelagic nekton, including compilation of observed species and descriptions of seasonal, regional and cross-shelf diversity patterns. Zooplankton diversity in the GoMA is characterized by spatial differences in community composition among the neritic environment, the coastal shelf, and deep offshore waters. Copepod diversity increased with depth on the Scotian Shelf. On the coastal shelf of the western Gulf of Maine, the number of higher-level taxonomic groups declined with distance from shore, reflecting more nearshore meroplankton. Copepod diversity increased in late summer, and interdecadal diversity shifts were observed, including a period of higher diversity in the 1990s. Changes in species diversity were greatest on interannual scales, intermediate on seasonal scales, and smallest across regions, in contrast to abundance patterns, suggesting that zooplankton diversity may be a more sensitive indicator of ecosystem response to interannual climate variation than zooplankton abundance. Local factors such as bathymetry, proximity of the coast, and advection probably drive zooplankton and pelagic nekton diversity patterns in the GoMA, while ocean-basin-scale diversity patterns probably contribute to the increase in diversity at the Scotian Shelf break, a zone of mixing between the cold-temperate community of the shelf and the warm-water community offshore. Pressing research needs include establishment of a comprehensive system for observing change in zooplankton and pelagic nekton diversity, enhanced observations of "underknown'' but important functional components of the ecosystem, population and metapopulation studies, and development of analytical modeling tools to enhance understanding of diversity patterns and drivers. Ultimately, sustained observations and modeling analysis of biodiversity must be effectively communicated to managers and incorporated into ecosystem approaches for management of GoMA living marine resources.

Structure-Function Analysis of the HrpB2-HrcU Interaction in the Xanthomonas citri Type III Secretion System

Bacterial type III secretion systems deliver protein virulence factors to host cells. Here we characterize the interaction between HrpB2, a small protein secreted by the Xanthomonas citri subsp. citri type III secretion system, and the cytosolic domain of the inner membrane protein HrcU, a paralog of the flagellar protein FlhB. We show that a recombinant fragment corresponding to the C-terminal cytosolic domain of HrcU produced in E. coli suffers cleavage within a conserved Asn264-Pro265-Thr266-His267 (NPTH) sequence. A recombinant HrcU cytosolic domain with N264A, P265A, T266A mutations at the cleavage site (HrcU(AAAH)) was not cleaved and interacted with HrpB2. Furthermore, a polypeptide corresponding to the sequence following the NPTH cleavage site also interacted with HrpB2 indicating that the site for interaction is located after the NPTH site. Non-polar deletion mutants of the hrcU and hrpB2 genes resulted in a total loss of pathogenicity in susceptible citrus plants and disease symptoms could be recovered by expression of HrpB2 and HrcU from extrachromossomal plasmids. Complementation of the Delta hrcU mutant with HrcU(AAAH) produced canker lesions similar to those observed when complemented with wild-type HrcU. HrpB2 secretion however, was significantly reduced in the Delta hrcU mutant complemented with HrcU(AAAH), suggesting that an intact and cleavable NPTH site in HrcU is necessary for total functionally of T3SS in X. citri subsp. citri. Complementation of the Delta hrpB2 X. citri subsp. citri strain with a series of hrpB2 gene mutants revealed that the highly conserved HrpB2 C-terminus is essential for T3SS-dependent development of citrus canker symptoms in planta.

Safety function analysis in an industrial production process

Dissertação para obtenção do Grau de Mestre em Engenharia e Gestão Industrial

STRUCTURE-FUNCTION ANALYSIS OF MULTI-COPPER OXIDASES

Dissertation presented to obtain the Ph.D degree in Biochemistry, Structural Biochemistry

Application of discriminant function analysis and change-point problem in dating volcanic ashes

The application of Discriminant function analysis (DFA) is not a new idea in the studyof tephrochrology. In this paper, DFA is applied to compositional datasets of twodifferent types of tephras from Mountain Ruapehu in New Zealand and MountainRainier in USA. The canonical variables from the analysis are further investigated witha statistical methodology of change-point problems in order to gain a betterunderstanding of the change in compositional pattern over time. Finally, a special caseof segmented regression has been proposed to model both the time of change and thechange in pattern. This model can be used to estimate the age for the unknown tephrasusing Bayesian statistical calibration

Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription.

The transcription factors TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound preinitiation complex, whereas Brf1 and Brf2 are involved, as part of activities also containing TBP and Bdp1 and referred to here as Brf1-TFIIIB and Brf2-TFIIIB, in the recruitment of Pol III. Brf1-TFIIIB recruits Pol III to type 1 and 2 promoters and Brf2-TFIIIB to type 3 promoters such as the human U6 promoter. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1. Here we have tested truncated Brf2, as well as Brf2/TFIIB chimeric proteins for U6 transcription and for assembly of U6 preinitiation complexes. Our results characterize functions of various human Brf2 domains and reveal that the C-terminal domain is required for efficient association of the protein with U6 promoter-bound TBP and SNAP(c), a type 3 promoter-specific transcription factor, and for efficient recruitment of Bdp1. This in turn suggests that the C-terminal extensions in Brf1 and Brf2 are crucial to specific recruitment of Pol III over Pol II.

Structure-function analysis of SOCSI mediated Growth arrest

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Application of discriminant function analysis and change-point problem in dating volcanic ashes

The application of Discriminant function analysis (DFA) is not a new idea in the study of tephrochrology. In this paper, DFA is applied to compositional datasets of two different types of tephras from Mountain Ruapehu in New Zealand and Mountain Rainier in USA. The canonical variables from the analysis are further investigated with a statistical methodology of change-point problems in order to gain a better understanding of the change in compositional pattern over time. Finally, a special case of segmented regression has been proposed to model both the time of change and the change in pattern. This model can be used to estimate the age for the unknown tephras using Bayesian statistical calibration

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

The poliovirus cis-acting replication element (CRE) templates the uridylylation of VPg, the protein primer for genome replication. The CRE is a highly conserved structural RNA element in the enteroviruses and located within the polyprotein-coding region of the genome. We have determined the native structure of the CRE, defined the regions of the structure critical for activity, and investigated the influence of genomic location on function. Our results demonstrate that a 14-nucleotide unpaired terminal loop, presented on a suitably stable stem, is all that is required for function. These conclusions complement the recent analysis of the 14-nucleotide terminal loop in the CRE of human rhinovirus type 14. The CRE can be translocated to the 5' noncoding region of the genome, at least 3.7-kb distant from the native location, without adversely influencing activity, and CRE duplications do not adversely influence replication. We do not have evidence for a specific interaction between the CRE and the RNA-binding 3CD(pro) complex, an essential component of the uridylylation reaction, and the mechanism by which the CRE is coordinated and orientated during the reaction remains unclear. These studies provide a detailed overview of the structural determinants required for CRE function, and will facilitate a better understanding of the requirements for picornavirus replication.

Evaluation of Philips and Ziegler-Natta high-density polyethylene degradation during processing in an internal mixer using the chain scission and branching distribution function analysis

The oxidative and thermo-mechanical degradation of HDPE was studied during processing in an internal mixer under two conditions: totally and partially filled chambers, which provides lower and higher concentrations of oxygen, respectively. Two types of HDPEs, Phillips and Ziegler-Natta, having different levels of terminal vinyl unsaturations were analyzed. Materials were processed at 160, 200, and 240 degrees C. Standard rheograrns using a partially filled chamber showed that the torque is much more unstable in comparison to a totally filled chamber which provides an environment depleted of oxygen. Carbonyl and transvinylene group concentrations increased, whereas vinyl group concentration decreased with temperature and oxygen availability. Average number of chain scission and branching (n(s)) was calculated from MWD curves and its plotting versus functional groups' concentration showed that chain scission or branching takes place depending upon oxygen content and vinyl groups' consumption. Chain scission and branching distribution function (CSBDF) values showed that longer chains undergo chain scission easier than shorter ones due to their higher probability of entanglements. This yields macroradicals that react with the vinyl terminal unsaturations of other chains producing chain branching. Shorter chains are more mobile, not suffering scission but instead are used for grafting the macroradicals, increasing the molecular weight. Increase in the oxygen concentration, temperature, and vinyl end groups' content facilitates the thermo-mechanical degradation reducing the amount of both, longer chains via chain scission and shorter chains via chain branching, narrowing the polydispersity. Phillips HDPE produces a higher level of chain branching than the Ziegler-Natta's type at the same processing condition. (c) 2006 Elsevier Ltd. All rights reserved.

Velocity structure and seismic anisotropy in the crust and upper mantle from Receiver Function analysis: three case studies in Italy

The research for this PhD project consisted in the application of the RFs analysis technique to different data-sets of teleseismic events recorded at temporary and permanent stations located in three distinct study regions: Colli Albani area, Northern Apennines and Southern Apennines. We found some velocity models to interpret the structures in these regions, which possess very different geologic and tectonics characteristics and therefore offer interesting case study to face. In the Colli Albani some of the features evidenced in the RFs are shared by all the analyzed stations: the Moho is almost flat and is located at about 23 km depth, and the presence of a relatively shallow limestone layer is a stable feature; contrariwise there are features which vary from station to station, indicating local complexities. Three seismic stations, close to the central part of the former volcanic edifice, display relevant anisotropic signatures­­­ with symmetry axes consistent with the emplacement of the magmatic chamber. Two further anisotropic layers are present at greater depth, in the lower crust and the upper mantle, respectively, with symmetry axes directions related to the evolution of the volcano complex. In Northern Apennines we defined the isotropic structure of the area, finding the depth of the Tyrrhenian (almost 25 km and flat) and Adriatic (40 km and dipping underneath the Apennines crests) Mohos. We determined a zone in which the two Mohos overlap, and identified an anisotropic body in between, involved in the subduction and going down with the Adiratic Moho. We interpreted the downgoing anisotropic layer as generated by post-subduction delamination of the top-slab layer, probably made of metamorphosed crustal rocks caught in the subduction channel and buoyantly rising toward the surface. In the Southern Apennines, we found the Moho depth for 16 seismic stations, and highlighted the presence of an anisotropic layer underneath each station, at about 15-20 km below the whole study area. The moho displays a dome-like geometry, as it is shallow (29 km) in the central part of the study area, whereas it deepens peripherally (down to 45 km); the symmetry axes of anisotropic layer, interpreted as a layer separating the upper and the lower crust, show a moho-related pattern, indicated by the foliation of the layer which is parallel to the Moho trend. Moreover, due to the exceptional seismic event occurred on April 6th next to L’Aquila town, we determined the Vs model for two station located next to the epicenter. An extremely high velocity body is found underneath AQU station at 4-10 km depth, reaching Vs of about 4 km/s, while this body is lacking underneath FAGN station. We compared the presence of this body with other recent works and found an anti-correlation between the high Vs body, the max slip patches and earthquakes distribution. The nature of this body is speculative since such high velocities are consistent with deep crust or upper mantle, but can be interpreted as a as high strength barrier of which the high Vs is a typical connotation.