Strain variation in ppGpp concentration and RpoS levels in laboratory strains of Escherichia coli K-12

Laboratory strains and natural isolates of Escherichia coli differ in their level of stress resistance due to strain variation in the level of the sigma factor sigma(S) (or RpoS), the transcriptional master controller of the general stress response. We found that the high level of RpoS in one laboratory strain (MC4100) was partially dependent on an elevated basal level of ppGpp, an alarmone responding to stress and starvation. The elevated ppGpp was caused by two mutations in spoT, a gene associated with ppGpp synthesis and degradation. The nature of the spoT allele influenced the level of ppGpp in both MC4100 and another commonly used K-12 strain, MG1655. Introduction of the spoT mutation into MG1655 also resulted in an increased level of RpoS, but the amount of RpoS was lower in MG1655 than in MC4100 with either the wild-type or mutant spoT allele. In both MC4100 and MG1655, high ppGpp concentration increased RpoS levels, which in turn reduced growth with poor carbon sources like acetate. The growth inhibition resulting from elevated ppGpp was relieved by rpoS mutations. The extent of the growth inhibition by ppGpp, as well as the magnitude of the relief by rpoS mutations, differed between MG1655 and MC4100. These results together suggest that spoT mutations represent one of several polymorphisms influencing the strain variation of RpoS levels. Stress resistance was higher in strains with the spoT mutation, which is consistent with the conclusion that microevolution affecting either or both ppGpp and RpoS can reset the balance between self-protection and nutritional capability, the SPANC balance, in individual strains of E coli.

Infectious bronchitis virus: detection and vaccine Strain differentiation by semi-nested RT-PCR

A semi-nested reverse transcription-polymerase chain reaction (Semi-N-RT-PCR) was developed and used to detect the S glycoprotein gene of infectious bronchitis virus (IBV) strains and to discriminate H120 vaccine strain from other strains. Viral RNA was extracted from the allantoic fluid of chicken embryos and from tissues of chickens experimentally infected with different strains of IBV. Amplification and identification of the viral RNA was performed using two sets of primers complementary to a region of the S glycoprotein gene in the Semi-N-RT-PCR assay. The pair of primers used in the first PCR consisted of universal oligonucleotides flanking a more variable region of S1-S2 gene. The second primer pair was used in the Semi-N-RT-PCR and was comprised of one of the primers from the first universal pair together with either another universal internal oligolucleotide or a oligonucleotide sequence specific for the H120 strain of IBV. The universal primers detected all reference IBV strains and field isolates tested herein. The Semi-N-RT-PCR had high sensitivity and specificity, and was able to differentiate the H120 vaccine strain from other reference IBV strains; including M41 strain. All tissue samples collected from chickens experimentally infected with H120 or M41 strains were positive in the semi-nested RT-PCR using universal primers, while only the H120-infected tissue samples were amplified by the set of primers containing the H120-oligonucleotide. In conclusion, the ability of Semi-N-RT-PCR to detect distinct IBV strains and preliminarily discriminate the vaccine strain (H120) closes a diagnostic gap and offers the opportunity to use comprehensive PCR procedures for the IBV diagnosis.

Effect of axial loads on implanted-supported partial fixed prostheses by strain gauge analysis

Objectives: The present study used strain gauge analysis to perform an in vitro evaluation of the effect of axial loading on 3 elements of implant-supported partial fixed prostheses, varying the type of prosthetic cylinder and the loading points. Material and methods: Three internal hexagon implants were linearly embedded in a polyurethane block. Microunit abutments were connected to the implants applying a torque of 20 Ncm, and prefabricated Co-Cr cylinders and plastic prosthetic cylinders were screwed onto the abutments, which received standard patterns cast in Co-Cr alloy (n=5). Four strain gauges (SG) were bonded onto the surface of the block tangentially to the implants, SG 01 mesially to implant 1, SG 02 and SG 03 mesially and distally to implant 2, respectively, and SG 04 distally to implant 3. Each metallic structure was screwed onto the abutments with a 10 Ncm torque and an axial load of 30 kg was applied at five predetermined points (A, B, C, D, E). The data obtained from the strain gauge analyses were analyzed statistically by RM ANOVA and Tukey's test, with a level of significance of p<0.05. Results: There was a significant difference for the loading point (p=0.0001), with point B generating the smallest microdeformation (239.49 mu epsilon) and point D the highest (442.77 mu epsilon). No significant difference was found for the cylinder type (p=0.748). Conclusions: It was concluded that the type of cylinder did not affect in the magnitude of microdeformation, but the axial loading location influenced this magnitude.

Machined and plastic copings in three-element prostheses with different types of implant-abutment joints: a strain gauge comparative analysis

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

Effect of axial loads on implant-supported partial fixed prostheses by strain gauge analysis

Objectives: The present study used strain gauge analysis to perform an in vitro evaluation of the effect of axial loading on 3 elements of implant-supported partial fixed prostheses, varying the type of prosthetic cylinder and the loading points. Material and methods: Three internal hexagon implants were linearly embedded in a polyurethane block. Microunit abutments were connected to the implants applying a torque of 20 Ncm, and prefabricated Co-Cr cylinders and plastic prosthetic cylinders were screwed onto the abutments, which received standard patterns cast in Co-Cr alloy (n = 5). Four strain gauges (SG) were bonded onto the surface of the block tangentially to the implants, SG 01 mesially to implant 1, SG 02 and SG 03 mesially and distally to implant 2, respectively, and SG 04 distally to implant 3. Each metallic structure was screwed onto the abutments with a 10 Ncm torque and an axial load of 30 kg was applied at five predetermined points (A, B, C, D, E). The data obtained from the strain gauge analyses were analyzed statistically by RM ANOVA and Tukey's test, with a level of significance of p<0.05. Results: There was a significant difference for the loading point (p=0.0001), with point B generating the smallest microdeformation (239.49 με) and point D the highest (442.77 με). No significant difference was found for the cylinder type (p=0.748). Conclusions: It was concluded that the type of cylinder did not affect in the magnitude of microdeformation, but the axial loading location influenced this magnitude.

Microstrain Around Dental Implants Supporting Fixed Partial Prostheses Under Axial and Non-Axial Loading Conditions, In Vitro Strain Gauge Analysis

The current study used strain gauge analysis to perform an in vitro evaluation of the effect of axial and non-axial loading on implant-supported fixed partial prostheses, varying the implant placement configurations and the loading points. Three internal hexagon implants were embedded in the center of each polyurethane block with in-line and offset placements. Microunit abutments were connected to the implants using a torque of 20 N.cm, and plastic prosthetic cylinders were screwed onto the abutments, which received standard patterns cast in Co-Cr alloy (n = 10). Four strain gauges (SGs) were bonded onto the surfaces of the blocks, tangentially to the implants: SG 01 mesially to implant 1, SG 02 and SG 03 mesially and distally to implant 2, respectively, and SG 04 distally to implant 3. Each metallic structure was screwed onto the abutments using a 10-N.cm torque, and axial and non-axial loads of 30 kg were applied at 5 predetermined points. The data obtained from the strain gauge analyses were analyzed statistically through the repeated measures analysis of variance and the Tukey test, with a conventional level of significance of P < 0.05. The results showed a statistically significant difference for the loading point (P = 0.0001), with point E (nonaxial) generating the highest microstrain (327.67 mu epsilon) and point A (axial) generating the smallest microstrain (208.93 mu epsilon). No statistically significant difference was found for implant placement configuration (P = 0.856). It was concluded that the offset implant placement did not reduce the magnitude of microstrain around the implants under axial and non-axial loading conditions, although loading location did influence this magnitude.

Bone stress and strain after use of a miniplate for molar protraction and uprighting: a 3-dimensional finite element analysis

The aim of this study was to use the finite element method to evaluate the distribution of stresses and strains on the local bone tissue adjacent to the miniplate used for anchorage of orthodontic forces. Methods: A 3-dimensional model composed of a hemimandible and teeth was constructed using dental computed tomographic images, in which we assembled a miniplate with fixation screws. The uprighting and mesial movements of the mandibular second molar that was anchored with the miniplate were simulated. The miniplate was loaded with horizontal forces of 2, 5, and 15 N. A moment of 11.77 N.mm was also applied. The stress and strain distributions were analyzed, and their correlations with the bone remodeling criteria and miniplate stability were assessed. Results: When orthodontic loads were applied, peak bone strain remained within the range of bone homeostasis (100-1500 mu m strain) with a balance between bone formation and resorption. The maximum deformation was found to be 1035 mu m strain with a force of 5 N. At a force of 15 N, bone resorption was observed in the region of the screws. Conclusions: We observed more stress concentration around the screws than in the cancellous bone. The levels of stress and strain increased when the force was increased but remained within physiologic levels. The anchorage system of miniplate and screws could withstand the orthodontic forces, which did not affect the stability of the miniplate.

The influence of anthropometric factors on postural balance: the relationship between body composition and posturographic measurements in young adults

OBJECTIVE: The aim of the present study was to evaluate the influence of anthropometric characteristics and gender on postural balance in adults. One hundred individuals were examined (50 males, 50 females; age range 20-40 years). METHODS: The following body composition measurements were collected (using bone densitometry measurements): fat percentage (% fat), tissue (g), fat (g), lean mass (g), bone mineral content (g), and bone mineral density (g/cm(2)). In addition, the following anthropometric measurements were collected: body mass (kg), height (cm), length of the trunk-cephalic region (cm), length of the lower limbs (cm) and length of the upper limbs (cm). The following indices were calculated: body mass index (kg/m(2)), waist-hip ratio and the support base (cm 2). Also, a postural balance test was performed using posturography variables with open and closed eyes. RESULTS: The analysis revealed poor correlations between postural balance and the anthropometric variables. A multiple linear regression analysis demonstrated that the whole group (female and male) height explained 12% of the medial-lateral displacement, 10% of the speed of oscillation, and 11% of the displacement area. The length of the trunk-cephalic length explained 6% of the displacement in the anteroposterior direction. With eyes closed, the support base and height explained 18% of the medial displacement, and the lateral height explained 10% of the displacement speed and 5% of the scroll area. CONCLUSION: Measured using posturography, the postural balance was only slightly influenced by the anthropometric variables, both with open and closed eyes. Height was the anthropometric variable that most influenced postural balance, both in the whole group and separately for each gender. Postural balance was more influenced by anthropometric factors in males than females.

Structural and strain analysis in the Late Paleozoic coastal accretionary wedge of central Chile

Abstract In this study structural and finite strain data are used to explore the tectonic evolution and the exhumation history of the Chilean accretionary wedge. The Chilean accretionary wedge is part of a Late Paleozoic subduction complex that developed during subduction of the Pacific plate underneath South America. The wedge is commonly subdivided into a structurally lower Western Series and an upper Eastern Series. This study shows the progressive development of structures and finite strain from the least deformed rocks in the eastern part of the Eastern Series of the accretionary wedge to higher grade schist of the Western Series at the Pacific coast. Furthermore, this study reports finite-strain data to quantify the contribution of vertical ductile shortening to exhumation. Vertical ductile shortening is, together with erosion and normal faulting, a process that can aid the exhumation of high-pressure rocks. In the east, structures are characterized by upright chevron folds of sedimentary layering which are associated with a penetrative axial-plane foliation, S1. As the F1 folds became slightly overturned to the west, S1 was folded about recumbent open F2 folds and an S2 axial-plane foliation developed. Near the contact between the Western and Eastern Series S2 represents a prominent subhorizontal transposition foliation. Towards the structural deepest units in the west the transposition foliation became progressively flat lying. Finite-strain data as obtained by Rf/Phi and PDS analysis in metagreywacke and X-ray texture goniometry in phyllosilicate-rich rocks show a smooth and gradual increase in strain magnitude from east to west. There are no evidences for normal faulting or significant structural breaks across the contact of Eastern and Western Series. The progressive structural and strain evolution between both series can be interpreted to reflect a continuous change in the mode of accretion in the subduction wedge. Before ~320-290 Ma the rocks of the Eastern Series were frontally accreted to the Andean margin. Frontal accretion caused horizontal shortening and upright folds and axial-plane foliations developed. At ~320-290 Ma the mode of accretion changed and the rocks of the Western Series were underplated below the Andean margin. This basal accretion caused a major change in the flow field within the wedge and gave rise to vertical shortening and the development of the penetrative subhorizontal transposition foliation. To estimate the amount that vertical ductile shortening contributed to the exhumation of both units finite strain is measured. The tensor average of absolute finite strain yield Sx=1.24, Sy=0.82 and Sz=0.57 implying an average vertical shortening of ca. 43%, which was compensated by volume loss. The finite strain data of the PDS measurements allow to calculate an average volume loss of 41%. A mass balance approximates that most of the solved material stays in the wedge and is precipitated in quartz veins. The average of relative finite strain is Sx=1.65, Sy=0.89 and Sz=0.59 indicating greater vertical shortening in the structurally deeper units. A simple model which integrates velocity gradients along a vertical flow path with a steady-state wedge is used to estimate the contribution of deformation to ductile thinning of the overburden during exhumation. The results show that vertical ductile shortening contributed 15-20% to exhumation. As no large-scale normal faults have been mapped the remaining 80-85% of exhumation must be due to erosion.

The role of bifidobacteria in newborn health and the intestinal microbial balance

Gut microbial acquisition during the early stage of life is an extremely important event since it affects the health status of the host. In this contest the healthy properties of the genus Bifidobacterium have a central function in newborns. The aim of this thesis was to explore the dynamics of the gut microbial colonization in newborns and to suggest possible strategies to maintain or restore a correct balance of gut bacterial population in infants. The first step of this work was to review the most recent studies on the use of probiotics and prebiotics in infants. Secondly, in order to prevent or treat intestinal disorders that may affect newborns, the capability of selected Bifidobacterium strains to reduce the amount of Enterobacteriaceae and against the infant pathogen Streptococcus agalactiae was evaluated in vitro. Furthermore, the ability of several commercial fibers to stimulate selectively the growth of bifidobacterial strains was checked. Finally, the gut microbial composition in the early stage of life in response to the intrapartum antibiotic prophylaxis (IAP) against group B Streptococcus was studied using q-PCR, DGGE and next generation sequencing. The results globally showed that Bifidobacterium breve B632 strain is the best candidate for the use in a synbiotic product coupled to a mixture of two selected prebiotic fibers (galactooligosaccharides and fructooligosaccharides) for gastrointestinal disorders in infants. Moreover, the early gut microbial composition was affected by IAP treatment with infants showing lower counts of Bifidobacterium spp. and Bacteroides spp. coupled to a decrement of biodiversity of bacteria, compared to control infants. These studies have shown that IAP could affect the early intestinal balance in infants and they have paved the way to the definition of new strategies alternative to antibiotic treatment to control GBS infection in pregnant women.

Integration of computational models and experimental characterization to study internal frost damage in cementitious materials

The objective of this doctoral research is to investigate the internal frost damage due to crystallization pore pressure in porous cement-based materials by developing computational and experimental characterization tools. As an essential component of the U.S. infrastructure system, the durability of concrete has significant impact on maintenance costs. In cold climates, freeze-thaw damage is a major issue affecting the durability of concrete. The deleterious effects of the freeze-thaw cycle depend on the microscale characteristics of concrete such as the pore sizes and the pore distribution, as well as the environmental conditions. Recent theories attribute internal frost damage of concrete is caused by crystallization pore pressure in the cold environment. The pore structures have significant impact on freeze-thaw durability of cement/concrete samples. The scanning electron microscope (SEM) and transmission X-ray microscopy (TXM) techniques were applied to characterize freeze-thaw damage within pore structure. In the microscale pore system, the crystallization pressures at sub-cooling temperatures were calculated using interface energy balance with thermodynamic analysis. The multi-phase Extended Finite Element Modeling (XFEM) and bilinear Cohesive Zone Modeling (CZM) were developed to simulate the internal frost damage of heterogeneous cement-based material samples. The fracture simulation with these two techniques were validated by comparing the predicted fracture behavior with the captured damage from compact tension (CT) and single-edge notched beam (SEB) bending tests. The study applied the developed computational tools to simulate the internal frost damage caused by ice crystallization with the two dimensional (2-D) SEM and three dimensional (3-D) reconstructed SEM and TXM digital samples. The pore pressure calculated from thermodynamic analysis was input for model simulation. The 2-D and 3-D bilinear CZM predicted the crack initiation and propagation within cement paste microstructure. The favorably predicted crack paths in concrete/cement samples indicate the developed bilinear CZM techniques have the ability to capture crack nucleation and propagation in cement-based material samples with multiphase and associated interface. By comparing the computational prediction with the actual damaged samples, it also indicates that the ice crystallization pressure is the main mechanism for the internal frost damage in cementitious materials.

Cylinder wall waste heat recovery from liquid-cooled internal combustion engines utilizing thermoelectric generators

This report is a dissertation proposal that focuses on the energy balance within an internal combustion engine with a unique coolant-based waste heat recovery system. It has been predicted by the U.S. Energy Information Administration that the transportation sector in the United States will consume approximately 15 million barrels per day in liquid fuels by the year 2025. The proposed coolant-based waste heat recovery technique has the potential to reduce the yearly usage of those liquid fuels by nearly 50 million barrels by only recovering even a modest 1% of the wasted energy within the coolant system. The proposed waste heat recovery technique implements thermoelectric generators on the outside cylinder walls of an internal combustion engine. For this research, one outside cylinder wall of a twin cylinder 26 horsepower water-cooled gasoline engine will be implemented with a thermoelectric generator surrogate material. The vertical location of these TEG surrogates along the water jacket will be varied along with the TEG surrogate thermal conductivity. The aim of this proposed dissertation is to attain empirical evidence of the impact, including energy distribution and cylinder wall temperatures, of installing TEGs in the water jacket area. The results can be used for future research on larger engines and will also assist with proper TEG selection to maximize energy recovery efficiencies.

Quantitative 3D strain analysis in analogue experiments: Integration of X-ray computed tomography and digital volume correlation techniques

The combination of scaled analogue experiments, material mechanics, X-ray computed tomography (XRCT) and Digital Volume Correlation techniques (DVC) is a powerful new tool not only to examine the 3 dimensional structure and kinematic evolution of complex deformation structures in scaled analogue experiments, but also to fully quantify their spatial strain distribution and complete strain history. Digital image correlation (DIC) is an important advance in quantitative physical modelling and helps to understand non-linear deformation processes. Optical non-intrusive (DIC) techniques enable the quantification of localised and distributed deformation in analogue experiments based either on images taken through transparent sidewalls (2D DIC) or on surface views (3D DIC). X-ray computed tomography (XRCT) analysis permits the non-destructive visualisation of the internal structure and kinematic evolution of scaled analogue experiments simulating tectonic evolution of complex geological structures. The combination of XRCT sectional image data of analogue experiments with 2D DIC only allows quantification of 2D displacement and strain components in section direction. This completely omits the potential of CT experiments for full 3D strain analysis of complex, non-cylindrical deformation structures. In this study, we apply digital volume correlation (DVC) techniques on XRCT scan data of “solid” analogue experiments to fully quantify the internal displacement and strain in 3 dimensions over time. Our first results indicate that the application of DVC techniques on XRCT volume data can successfully be used to quantify the 3D spatial and temporal strain patterns inside analogue experiments. We demonstrate the potential of combining DVC techniques and XRCT volume imaging for 3D strain analysis of a contractional experiment simulating the development of a non-cylindrical pop-up structure. Furthermore, we discuss various options for optimisation of granular materials, pattern generation, and data acquisition for increased resolution and accuracy of the strain results. Three-dimensional strain analysis of analogue models is of particular interest for geological and seismic interpretations of complex, non-cylindrical geological structures. The volume strain data enable the analysis of the large-scale and small-scale strain history of geological structures.

Mass Balance and Accumulation Rate Across Siple Dome, West Antarctica

Snow-accumulation rates and rates of ice-thickness change (mass balance) are studied at several sites on Siple Dome, West Antarctica. Accumulation rates are derived from analyses of gross beta radioactivity in shallow firn cores located along a 60 km transect spanning both flanks and the crest of the dome. There is a north-south gradient in snow-accumulation rate across the dome that is consistent with earlier radar mapping of internal stratigraphy. Orographic processes probably control this distribution. Mass balance is inferred from the difference between global positioning system (GPS)-derived vertical velocities and snow-accumulation rates for sites close to the firn-core locations. Results indicate that there is virtually no net thickness change at four of the five sites. The exception is at the northernmost site where a small amount of thinning is detected, that appears to be inconsistent with other studies. A possible cause of this anomalous thinning is recent retreat of the grounding line of Ice Stream D.

Evidence for a Frozen Bed, Byrd Glacier, Antarctica

Ice thickness, computed within the fjord region of Byrd Glacier on the assumptions that Byrd Glacier is in mass-balance equilibrium and that ice velocity is entirely due to basal sliding, are on average 400 m less than measured ice thicknesses along a radio-echo profile. We consider four explanations for these differences: (1) active glacier ice is separated from a zone of stagnant ice near the base of the glacier by a shear zone at depth; (2) basal melting rates are some 8 m/yr; (3) internal shear occurs with no basal sliding in much of the region above the grounding zone; or (4) internal creep and basal sliding contribute to the flow velocity in varying proportions above the grounding zone. Large gradients of surface strain rate seem to invalidate the first explanation. Computed values of basal shear stress (140 to 200 kPa) provide insufficient frictional heat to melt the ice demanded by the second explanation. Both the third and fourth explanations were examined by making simplifying assumptions that prevented a truly quantitative evaluation of their merit. Nevertheless, there is no escaping the qualitative conclusion that internal shear contributes strongly to surface velocities measured on Byrd Glacier, as is postulated in both these explanations.