Stress responses in mycobacteria

Mycobacterium tuberculosis is a successful pathogen that overcomes numerous challenges presented by the immune system of the host. This bacterium usually establishes a chronic infection in the host where it may silently persist inside a granuloma until, a failure in host defenses, leads to manifestation of the disease. None of the conventional anti-tuberculosis drugs are able to target these persisting bacilli. Development of drugs against such persisting bacilli is a constant challenge since the physiology of these dormant bacteria is still not understood at the molecular level. Some evidence suggests that the in vivo environment encountered by the persisting bacteria is anoxic and nutritionally starved. Based on these assumptions, anaerobic and starved cultures are used as models to study the molecular basis of dormancy. This review outlines the problem of persistence of M. tuberculosis and the various in vitro models used to study mycobacterial latency. The basis of selecting the nutritional starvation model has been outlined here. Also, the choice of M. smegmatis as a model suitable for studying mycobacterial latency is discussed. Lastly, general issues related to oxidative stress and bacterial responses to it have been elaborated. We have also discussed general control of OxyR-mediated regulation and emphasized the processes which manifest in the absence of functional OxyR in the bacteria. Lastly, a new class of protein called Dps has been reviewed for its important role in protecting DNA under stress.

Catalytic activity of Peptidase N is required for adaptation of Escherichia coli to nutritional downshift and high temperature stress

Peptidase N (PepN), the sole M1 family member in Escherichia coli, displays broad substrate specificity and modulates stress responses: it lowers resistance to sodium salicylate (NaSal)-induced stress but is required during nutritional downshift and high temperature (NDHT) stress. The expression of PepN does not significantly change during different growth phases in LB or NaSal-induced stress; however, PepN amounts are lower during NDHT stress. To gain mechanistic insights on the roles of catalytic activity of PepN in modulating these two stress responses, alanine mutants of PepN replacing E264 (GAMEN motif) and E298 (HEXXH motif) were generated. There are no major structural changes between purified wild type (WT) and mutant proteins, which are catalytically inactive. Importantly, growth profiles of Delta pepN upon expression of WT or mutant proteins demonstrated the importance of catalytic activity during NDHT but not NaSal-induced stress. Further fluorescamine reactivity studies demonstrated that the catalytic activity of PepN is required to generate higher intracellular amounts of free N-terminal amino acids; consequently, the lower growth of Delta pepN during NDHT stress increases with high amounts of casamino acids. Together, this study sheds insights on the expression and functional roles of the catalytic activity of PepN during adaptation to NDHT stress. (C) 2012 Elsevier GmbH. All rights reserved.

Unstructured N Terminus of the RNA Polymerase II Subunit Rpb4 Contributes to the Interaction of Rpb4·Rpb7 Subcomplex with the Core RNA Polymerase II of Saccharomyces cerevisiae

Two subunits of eukaryotic RNA polymerase II, Rpb7 and Rpb4, form a subcomplex that has counterparts in RNA polymerases I and III. Although a medium resolution structure has been solved for the 12-subunit RNA polymerase II, the relative contributions of the contact regions between the subcomplex and the core polymerase and the consequences of disrupting them have not been studied in detail. We have identified mutations in the N-terminal ribonucleoprotein-like domain of Saccharomyces cerevisiae Rpb7 that affect its role in certain stress responses, such as growth at high temperature and sporulation. These mutations increase the dependence of Rpb7 on Rpb4 for interaction with the rest of the polymerase. Complementation analysis and RNA polymerase pulldown assays reveal that the Rpb4 center dot Rbp7 subcomplex associates with the rest of the core RNA polymerase II through two crucial interaction points: one at the N-terminal ribonucleoprotein-like domain of Rpb7 and the other at the partially ordered N-terminal region of Rpb4. These findings are in agreement with the crystal structure of the 12-subunit polymerase. We show here that the weak interaction predicted for the N-terminal region of Rpb4 with Rpb2 in the crystal structure actually plays a significant role in interaction of the subcomplex with the core in vivo. Our mutant analysis also suggests that Rpb7 plays an essential role in the cell through its ability to interact with the rest of the polymerase.

A finite element analysis of quasistatic crack growth in a pressure sensitive constrained ductile layer

Polymeric adhesive layers are employed for bonding two components in a wide variety of technological applications, It has been observed that, unlike in metals, the yield behavior of polymers is affected by the state of hydrostatic stress. In this work, the effect of pressure sensitivity of yielding and layer thickness on quasistatic interfacial crack growth in a ductile adhesive layer is investigated. To this end, finite deformation, finite element analyses of a cracked sandwiched layer are carried out under plane strain, small-scale yielding conditions for a wide range of mode mixities. The Drucker-Prager constitutive equations are employed to represent the behavior of the layer. Crack propagation is simulated through a cohesive zone model, in which the interface is assumed to follow a prescribed traction-separation law. The results show that for a given mode mixity, the steady state Fracture toughness [K](ss) is enhanced as the degree of pressure sensitivity increases. Further, for a given level of pressure sensitivity, [K](ss) increases steeply as mode Il loading is approached. (C) 2000 Elsevier Science Ltd. All rights reserved.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Micropillar and macropillar compression responses of magnesium single crystals oriented for single slip or extension twinning

Uniaxial compression experiments were conducted on two magnesium (Mg) single crystals whose crystallographic orientations facilitate the deformation either by basal slip or by extension twinning. Specimen size effects were examined by conducting experiments on mu m- and mm-sized samples. A marked specimen size effect was noticed, with micropillars exhibiting significantly higher flow stress than bulk samples. Further, it is observed that the twin nucleation stress exerts strong size dependence, with micropillars requiring substantially higher stress than the bulk samples. The flow curves obtained on the bulk samples are smooth whereas those obtained from micropillars exhibit intermittent and precipitous stress drops. Electron backscattered diffraction and microstructural analyses of the deformed samples reveal that the plastic deformation in basal slip oriented crystals occurs only by slip while twin oriented crystals deform by both slip and twinning modes. The twin oriented crystals exhibit a higher strain hardening during plastic deformation when compared to the single slip oriented crystals. The strain hardening rate, theta, of twin oriented crystals is considerably greater in micropillars compared to the bulk single crystals, suggesting the prevalence of different work hardening mechanisms at these different sample sizes. (C) 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Families of asymptotic tensile crack tip stress fields in elastic-perfectly plastic single crystals

In this work, two families of asymptotic near-tip stress fields are constructed in an elastic-ideally plastic FCC single crystal under mode I plane strain conditions. A crack is taken to lie on the (010) plane and its front is aligned along the [(1) over bar 01] direction. Finite element analysis is first used to systematically examine the stress distributions corresponding to different constraint levels. The general framework developed by Rice (Mech Mater 6:317-335, 1987) and Drugan (J Mech Phys Solids 49:2155-2176, 2001) is then adopted to generate low triaxiality solutions by introducing an elastic sector near the crack tip. The two families of stress fields are parameterized by the normalized opening stress (tau(A)(22)/tau(o)) prevailing in the plastic sector in front of the tip and by the coordinates of a point where elastic unloading commences in stress space. It is found that the angular stress variations obtained from the analytical solutions show good agreement with finite element analysis.

Determination of mode 1 notch stress intensity factor by the photoelastic technique

The structural integrity of any member subjected to a load gets impaired due to the presence of cracks or crack-like defects. The notch severity is one of the several parameters that promotes the brittle fracture. The most severe one is an ideal crack with infinitesimal width and infinitesimal or zero root radius. Though analytical investigations can handle an ideal crack, experimental work, either to validate the analytical conclusions or to impose the bounds, needs to be carried out on models or specimens containing the cracks which are far from the ideal ones. Thus instead of an ideal crack with infinitesimal width the actual model will have a slot or a slit of finite width and instead of a crack ending in zero root radius, the model contains a slot having a finite root radius. Another factor of great significance at the root is the notch angle along which the transition from the slot to the root takes place. This paper is concerned with the photoelastic determination of the notch stress intensity factor in the case of a “crack” subjected to Mode 1 deformation.

Stress and strain-driven algorithmic formulations for finite strain viscoplasticity for hybrid and standard finite elements

This work deals with the formulation and implementation of finite deformation viscoplasticity within the framework of stress-based hybrid finite element methods. Hybrid elements, which are based on a two-field variational formulation, are much less susceptible to locking than conventional displacement-based elements. The conventional return-mapping scheme cannot be used in the context of hybrid stress methods since the stress is known, and the strain and the internal plastic variables have to be recovered using this known stress field.We discuss the formulation and implementation of the consistent tangent tensor, and the return-mapping algorithm within the context of the hybrid method. We demonstrate the efficacy of the algorithm on a wide range of problems.

Mycobacterial Stress Regulation: The Dps ``Twin Sister'' Defense Mechanism and Structure-Function Relationship

In this work, we have tried to emphasize the connection between mycobacterial growth and regulation of gene expression. Utilization of multiple carbon sources and diauxic growth helps bacteria to regulate gene expression at an optimum level so that the inhospitable conditions encountered during nutrient depletion can be circumvented. These aspects will be discussed with respect to mycobacterial growth in subsequent sections. Identification and characterization of genes induced under such conditions is helpful to understand the physiology of the bacterium. Although it is necessary to compare the total expression profile of proteins as they transit from vegetative growth to stationary phase, at times a lot of insights can be deciphered from the expression pattern of one or two proteins. We have compared the protein expression and sigma factor selectivity of two such proteins in M. smegmatis to understand the differential regulation of genes playing diverse function in the same species. Some newer insights on the structure and function of one of the Dps proteins are also explained.

Computation of Thermal Stress Intensity Factors for Bimaterial Interface Cracks Using Domain Integral Method

The concept of domain integral used extensively for J integral has been applied in this work for the formulation of J(2) integral for linear elastic bimaterial body containing a crack at the interface and subjected to thermal loading. It is shown that, in the presence of thermal stresses, the J(k) domain integral over a closed path, which does not enclose singularities, is a function of temperature and body force. A method is proposed to compute the stress intensity factors for bimaterial interface crack subjected to thermal loading by combining this domain integral with the J(k) integral. The proposed method is validated by solving standard problems with known solutions.

The Multifunctional PE_PGRS11 Protein from Mycobacterium tuberculosis Plays a Role in Regulating Resistance to Oxidative Stress

Mycobacterium tuberculosis utilizes unique strategies to survive amid the hostile environment of infected host cells. Infection-specific expression of a unique mycobacterial cell surface antigen that could modulate key signaling cascades can act as a key survival strategy in curtailing host effector responses like oxidative stress. We demonstrate here that hypothetical PE_PGRS11 ORF encodes a functional phosphoglycerate mutase. The transcriptional analysis revealed that PE_PGRS11 is a hypoxia-responsive gene, and enforced expression of PE_PGRS11 by recombinant adenovirus or Mycobacterium smegmatis imparted resistance to alveolar epithelial cells against oxidative stress. PE_PGRS11-induced resistance to oxidative stress necessitated the modulation of genetic signatures like induced expression of Bcl2 or COX-2. This modulation of specific antiapoptotic molecular signatures involved recognition of PE_PGRS11 by TLR2 and subsequent activation of the PI3K-ERK1/ 2-NF-kappa B signaling axis. Furthermore, PE_PGRS11 markedly diminished H2O2-induced p38 MAPK activation. Interestingly, PE_PGRS11 protein was exposed at the mycobacterial cell surface and was involved in survival of mycobacteria under oxidative stress. Furthermore, PE_PGRS11 displayed differential B cell responses during tuberculosis infection. Taken together, our investigation identified PE_PGRS11 as an in vivo expressed immunodominant antigen that plays a crucial role in modulating cellular life span restrictions imposed during oxidative stress by triggering TLR2-dependent expression of COX-2 and Bcl2. These observations clearly provide a mechanistic basis for the rescue of pathogenic Mycobacterium-infected lung epithelial cells from oxidative stress.

Interaction anisotropy and shear instability of aspirin polymorphs established by nanoindentation

Nanoindentation is applied to the two polymorphs of aspirin to examine and differentiate their interaction anisotropy and shear instability. Aspirin provides an excellent test system for the technique because: (i) polymorphs I and II exhibit structural similarity in two dimensions, thereby facilitating clear examination of the differences in mechanical response in relation to well-defined differences between the two crystal structures; (ii) single crystals of the metastable polymorph II have only recently become accessible; (iii) shear instability has been proposed for II. Different elastic moduli and hardness values determined for the two polymorphs are correlated with their crystal structures, and the interpretation is supported by measured thermal expansion coefficients. The stress-induced transformation of the metastable polymorph II to the stable polymorph I can be brought about rapidly by mechanical milling, and proceeds via a slip mechanism. This work establishes that nanoindentation provides ``signature'' responses for the two aspirin polymorphs, despite their very similar crystal structures. It also demonstrates the value of the technique to quantify stability relationships and phase transformations in molecular crystals, enabling a deeper understanding of polymorphism in the context of crystal engineering.

Tensile flow and work hardening behavior of hot cross-rolled AA7010 aluminum alloy sheets

The present work describes the tensile flow and work hardening behavior of a high strength 7010 aluminum alloy by constitutive relations. The alloy has been hot rolled by three different cross-rolling schedules. Room temperature tensile properties have been evaluated as a function of tensile axis orientation in the as-hot rolled as well as peak aged conditions. It is found that both the Ludwigson and a generalized Voce-Bergstrom relation adequately describe the tensile flow behavior of the present alloy in all conditions compared to the Hollomon relation. The variation in the Ludwigson fitting parameter could be correlated well with the microstructural features and anisotropic contribution of strengthening precipitates in the as-rolled and peak aged conditions, respectively. The hardening rate and the saturation stress of the first Voce-Bergstrom parameter, on the other hand, depend mainly on the crystallographic texture of the specimens. It is further shown that for the peak aged specimens the uniform elongation (epsilon(u)) derived from the Ludwigson relation matches well with the measured epsilon(u) irrespective of processing and loading directions. However, the Ludwigson fit overestimates the epsilon(u) in case of the as-rolled specimens. The Hollomon fit, on the other hand, predicts well the measured epsilon(u), of the as-rolled specimens but severely underestimates the epsilon(u), for the peak aged specimens. Contrarily, both the relations significantly overestimate the UTS of the as-rolled and the peak aged specimens. The Voce-Bergstrom parameters define the slope of e Theta-sigma plots in the stage-III regime when the specimens show a classical linear decrease in hardening rate in stage-III. Further analysis of work hardening behavior throws some light on the effect of texture on the dislocation storage and dynamic recovery.

Effect of Stress and Interface defects on Photo Luminescence of Si nano-crystals embedded in SiO2

Effect of stress and interface defects on photo luminescence property of a silicon nano-crystal (Si-nc) embedded in amorphous silicon dioxide (a-SiO2) are studied in this paper using a self-consistent quantum-continuum based modeling framework. Si-ncs or quantum dots show photoluminescence at room temperature. Whether its origin is due to Si-nc/a-SiO2 interface defects or quantum confinement of carriers in Si-nc is still an outstanding question. Earlier reports have shown that stresses greater than 12 GPa change the indirect energy band gap structure of bulk Si to a direct energy band gap structure. Such stresses are observed very often in nanostructures and these stresses influence the carrier confinement energy significantly. Hence, it is important to determine the effect of stress in addition to the structure of interface defects on photoluminescence property of Si-nc. In the present work, first a Si-nc embedded in a-SiO2 is constructed using molecular dynamics simulation framework considering the actual conditions they are grown so that the interface and residual stress in the structure evolves naturally during formation. We observe that the structure thus created has an interface of about 1 nm thick consisting of 41.95% of defective states mostly Sin+ (n = 0 to 3) coordination states. Further, both the Si-nc core and the embedding matrix are observed to be under a compressive strain. This residual strain field is applied in an effective mass k.p Hamiltonian formulation to determine the energy states of the carriers. The photo luminescence property computed based on the carrier confinement energy and interface energy states associated with defects will be analysed in details in the paper.