Reduction in DNA topoisomerase I level affects growth, phenotype and nucleoid architecture of Mycobacterium smegmatis

The steady-state negative supercoiling of eubacterial genomes is maintained by the action of DNA topoisomerases. Topoisomerase distribution varies in different species of mycobacteria. While Mycobacterium tuberculosis (Mtb) contains a single type I (Topol) and a single type II (Gyrase) enzyme, Mycobacterium smegmatis (Msm) and other members harbour additional relaxases. Topol is essential for Mtb survival. However, the necessity of Topol or other relaxases in Msm has not been investigated. To recognize the importance of Topol for growth, physiology and gene expression of Msm, we have developed a conditional knock-down strain of Topol in Msm. The Topol-depleted strain exhibited extremely slow growth and drastic changes in phenotypic characteristics. The cessation of growth indicates the essential requirement of the enzyme for the organism in spite of having additional DNA relaxation enzymes in the cell. Notably, the imbalance in Topol level led to the altered expression of topology modulatory proteins, resulting in a diffused nucleoid architecture. Proteomic and transcript analysis of the mutant indicated reduced expression of the genes involved in central metabolic pathways and core DNA transaction processes. RNA polymerase (RNAP) distribution on the transcription units was affected in the Topol-depleted cells, suggesting global alteration in transcription. The study thus highlights the essential requirement of Topol in the maintenance of cellular phenotype, growth characteristics and gene expression in mycobacteria. A decrease in Topol level led to altered RNAP occupancy and impaired transcription elongation, causing severe downstream effects.

Archaeometric evidence for the authenticity of the Jehoash inscription tablet

A gray, fine-grained arkosic sandstone tablet bearing an inscription in ancient Hebrew from the First Temple Period contains a rich assemblage of particles accumulated in the covering patina. Two types of patina cover the tablet: a thin layer of black to orange iron-oxide-rich layer, a product of micro-biogenic processes, and a light beige patina that contains feldspars, carbonate, iron oxide, subangular quartz grains, carbon ash particles and gold globules (1 to 4 microns [1 micron = 0.001 millimeter] in diameter). The patina covers the rock surface as well as the engraved lettering grooves and blankets and thus post-dates the incised inscription as well as a crack that runs across the stone and several of the engraved letters. Radiocarbon analyses of the carbon particles in the patina yield a calibrated radiocarbon age of 2340 to 2150 Cal BP. The presence of microcolonial fungi and associated pitting in the patina indicates slow growth over many years. The occurrence of pure gold globules and carbon ash particles is evidence of a thermal event in close proximity to the tablet (above 1000 degrees Celsius). This study supports the antiquity of the patina, which in turn, strengthens the contention that the inscription is authentic.

Torsional impact response of a penny-shaped interface crack in bonded materials with a graded material interlayer

In this paper, the dynamic response of a penny-shaped interface crack in bonded dissimilar homogeneous half-spaces is studied. It is assumed that the two materials are bonded together with such a inhomogeneous interlayer that makes the elastic modulus in the direction perpendicular to the crack surface is continuous throughout the space. The crack surfaces art assumed to be subjected to torsional impact loading. Laplace and Hankel integral transforms are applied combining with a dislocation density,function to reduce the mixed boundary value problem into a singular integral equation with a generalized Cauchy kernel in Laplace domain. By solving the singular integral equation numerically, and using a numerical Laplace inversion technique, the dynamic stress intensity factors art obtained. The influences of material properties and interlayer thickness on the dynamic stress intensity factor are investigated.

Effect of a laser pre-quenched steel substrate surface on the crack driving force in a coating-steel substrate system

A mechanical model of a coating/laser pre-quenched steel substrate specimen with a crack oriented perpendicular to the interface between the coating and the hardened layer is developed to quantify the effects of the residual stress and hardness gradient on the crack driving force in terms of the J-integral. It is assumed that the crack tip is in the middle of the hardened layer of the pre-quenched steel substrate. Using a composite double cantilever beam model, analytical solutions can be derived, and these can be used to quantify the effects of the residual stress and the hardness gradient resulting from the pre-quenched steel substrate surface on the crack driving force. A numerical example is presented to investigate how the residual compressive stress, the coefficient linking microhardness and yield strength and the Young's modulus ratio of the hardened layer to the coating influence the crack driving force for a given crack length. (C) 2007 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Atomistic simulations of crack nucleation and intergranular fracture in bulk nanocrystalline nickel

We report large scale molecular dynamics simulations of dynamic cyclic uniaxial tensile deformation of pure, fully dense nanocrystalline Ni, to reveal the crack initiation, and consequently intergranular fracture is the result of coalescence of nanovoids by breaking atomic bonds at grain boundaries and triple junctions. The results indicate that the brittle fracture behavior accounts for the transition from plastic deformation governed by dislocation to one that is grain-boundary dominant when the grain size reduces to the nanoscale. The grain-boundary mediated plasticity is also manifested by the new grain formation and growth induced by stress-assisted grain-boundary diffusion observed in this work. This work illustrates that grain-boundary decohesion is one of the fundamental deformation mechanisms in nanocrystalline Ni.

Subsonic interface crack with crack face contact

A steady-state subsonic interface crack propagating between an elastic solid and a rigid substrate with crack face contact is studied. Two cases with respective to the contact length are considered, i.e., semi-infinite and finite crack face contact. Different from a stationary or an open subsonic interface crack, stress singularity at the crack tip in the present paper is found to be non-oscillatory. Furthermore, in the semi-infinite contact case, the singularity of the stress field near the crack tip is less than 1/2. In the finite contact case, no singularity exists near the crack tip, but less than 1/2 singularity does at the end of the contact zone. In both cases, the singularity depends on the linear contact coefficient and the crack speed. Asymptotic solutions near the crack tip are given and analyzed. In order to satisfy the contact conditions, reasonable region of the linear contact coefficient is found. In addition, the solution predicts a non-zero-energy dissipation rate due to crack face contact.

Plastidic Phosphoglucose Isomerase Is an Important Determinant of Starch Accumulation in Mesophyll Cells, Growth, Photosynthetic Capacity, and Biosynthesis of Plastidic Cytokinins in Arabidopsis

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization of glucose-6-phosphate and fructose-6-phosphate. It is involved in glycolysis and in the regeneration of glucose-6-P molecules in the oxidative pentose phosphate pathway (OPPP). In chloroplasts of illuminated mesophyll cells PGI also connects the Calvin-Benson cycle with the starch biosynthetic pathway. In this work we isolated pgi1-3, a mutant totally lacking pPGI activity as a consequence of aberrant intron splicing of the pPGI encoding gene, PGI1. Starch content in pgi1-3 source leaves was ca. 10-15% of that of wild type (WT) leaves, which was similar to that of leaves of pgi1-2, a T-DNA insertion pPGI null mutant. Starch deficiency of pgi1 leaves could be reverted by the introduction of a sex1 null mutation impeding beta-amylolytic starch breakdown. Although previous studies showed that starch granules of pgi1-2 leaves are restricted to both bundle sheath cells adjacent to the mesophyll and stomata guard cells, microscopy analyses carried out in this work revealed the presence of starch granules in the chloroplasts of pgi1-2 and pgi1-3 mesophyll cells. RT-PCR analyses showed high expression levels of plastidic and extra-plastidic beta-amylase encoding genes in pgi1 leaves, which was accompanied by increased beta-amylase activity. Both pgi1-2 and pgi1-3 mutants displayed slow growth and reduced photosynthetic capacity phenotypes even under continuous light conditions. Metabolic analyses revealed that the adenylate energy charge and the NAD(P) H/NAD(P) ratios in pgi1 leaves were lower than those of WT leaves. These analyses also revealed that the content of plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway derived cytokinins (CKs) in pgi1 leaves were exceedingly lower than in WT leaves. Noteworthy, exogenous application of CKs largely reverted the low starch content phenotype of pgi1 leaves. The overall data show that pPGI is an important determinant of photosynthesis, energy status, growth and starch accumulation in mesophyll cells likely as a consequence of its involvement in the production of OPPP/glycolysis intermediates necessary for the synthesis of plastidic MEP-pathway derived hormones such as CKs.

Czochralski growth and crystal structure of cerium-doped Lu2Si2O7 scintillator

Cerium-doped lutetium pyrosilicate crystal, Ce:Lu2Si2O7 (Ce:LPS), was grown by the Czochralski method. The segregation coefficient of Ce3+ ion was studied by the ICP-AES method. X-ray diffraction analysis showed that the structure of Ce:LPS crystal was monoclinic symmetry with space group of C2/m. Perfect cleavage planes (110) and imperfect cleavage planes (001) were observed by optical microscope. The reasons why it is difficult to grow crack-free crystals were studied. After optimized growth parameters, a Ce:LPS crystal with dimension of Phi 25 x 30 mm was grown, which is colorless, high optical quality, cracking-free and no inclusions. The transmittance of Ce:LPS crystal from 380 to 800 nm is over 82% and there is no observable absorption. (c) 2005 Elsevier B.V. All rights reserved.

Using an inverse-logistic model to describe growth increments of blacklip abalone (Haliotis rubra) in Tasmania

A new description of growth in blacklip abalone (Haliotis rubra) with the use of an inverse-logistic model is introduced. The inverse-logistic model avoids the disadvantageous assumptions of either rapid or slow growth for small and juvenile individuals implied by the von Bertalanffy and Gompertz growth models, respectively, and allows for indeterminate growth where necessary. An inverse-logistic model was used to estimate the expected mean growth increment for different black-lip abalone populations around southern Tasmania, Australia. Estimates of the time needed for abalone to grow from settlement until recruitment (at 138 mm shell length) into the fishery varied from eight to nine years. The variability of the residuals about the predicted mean growth increments was described with either a second inverse-logistic relationship (standard deviation vs. initial length) or by a power relationship (standard deviation vs. predicted growth increment). The inverse-logistic model can describe linear growth of small and juvenile abalone (as observed in Tasmania), as well as a spectrum of growth possibilities, from determinate to indeterminate growth (a spectrum that would lead to a spread of maximum lengths).

Improving Shepherd's Length Composition Analysis (SLCA) method for growth parameter estimations

Shepherd's "weekly parametric" method for estimating the parameter L sub( infinity ) and K of the von Bertalanffy growth function from length-frequency data often fails to converge, and usually overestimates K. It is shown that this is due to overcounting of the frequencies associated with large, slow growing fish, and that both of these problems can be completely overcome by a simple change in the way the scoring function is formulated.

Age, growth and mortality of the toadfish, Halobatrachus didactylus (Schneider, 1801) (Pisces: Batrachoididae), in the Bay of Cádiz (southwestern Spain)

Age, growth and mortality of the toadfish, Halobatrachus didactylus, were determined by examination of the whole sagittal otoliths of fish sampled in the Bay of Cádiz (southwestern Spain) from March 1999 to March 2000. A total of 844 specimens (425 males, 416 females, and 3 of indeterminate sex), ranging from 95 to 470 mm in total length were examined. Eighty-nine percent of the otoliths could be read allowing an age estimation. The opaque zone was formed between April and May coincident with the maximum reproductive peak, while the translucent zone formed mainly in summer-fall (June to December). Maximum ages for males and females were 12 and 10 years, respectively. The samples were dominated by 2- to 6-year-old specimens. Males matured at an age of approximately 2 years and females at 3 years. Fish total length and otolith radius were closely related. The von Bertalanffy growth curve was used to describe growth. The parameters were derived from back-calculated length-at-age. Significant differences in the growth parameters were found between sexes. Although the growth analysis revealed that this species is slow-growing, males reached larger sizes than females. Females appeared to experience higher natural mortality rates than males.

An environmentally based growth model that uses finite difference calculus with maximum likelihood method: its application to the brackish water bivalve Corbicula japonica in Lake Abashiri, Japan

We present a growth analysis model that combines large amounts of environmental data with limited amounts of biological data and apply it to Corbicula japonica. The model uses the maximum-likelihood method with the Akaike information criterion, which provides an objective criterion for model selection. An adequate distribution for describing a single cohort is selected from available probability density functions, which are expressed by location and scale parameters. Daily relative increase rates of the location parameter are expressed by a multivariate logistic function with environmental factors for each day and categorical variables indicating animal ages as independent variables. Daily relative increase rates of the scale parameter are expressed by an equation describing the relationship with the daily relative increase rate of the location parameter. Corbicula japonica grows to a modal shell length of 0.7 mm during the first year in Lake Abashiri. Compared with the attain-able maximum size of about 30 mm, the growth of juveniles is extremely slow because their growth is less susceptible to environmental factors until the second winter. The extremely slow growth in Lake Abashiri could be a geographical genetic variation within C. japonica.

Description and growth of larval and pelagic juvenile pygmy rockfish (Sebastes wilsoni) (family Sebastidae)

A developmental series of larval and pelagic juvenile pygmy rockfish (Sebastes wilsoni) from central California is illustrated and described. Sebastes wilsoni is a non- commercially, but ecologically, important rockfish, and the ability to differentiate its young stages will aid researchers in population abundance studies. Pigment patterns, meristic characters, morphometric measurements, and head spination were recorded from specimens that ranged from 8.1 to 34.4 mm in standard length. Larvae were identified initially by meristic characters and the absence of ventral and lateral midline pigment. Pelagic juveniles developed a prominent pigment pattern of three body bars that did not extend to the ventral surface. Species identification was confirmed subsequently by using mitochondrial sequence data of four representative specimens of various sizes. As determined from the examination of otoliths, the growth rate of larval and pelagic juvenile pygmy rockfish was 0.28 mm/day, which is relatively slow in comparison to the growth rate of other species of Sebastes. These data will aid researchers in determining species abundance.

Radiometric validation of age, growth, and longevity for the blackgill rockfish (Sebastes melanostomus)

As nearshore fish populations decline, many commercial fishermen have shifted fishing effort to deeper continental slope habitats to target fishes for which biological information is limited. One such fishery that developed in the northeastern Pacific Ocean in the early 1980s was for the blackgill rockfish (Sebastes melanostomus), a deep-dwelling (300−800 m) species that congregates over rocky pinnacles, mainly from southern California to southern Oregon. Growth zone-derived age estimates from otolith thin sections were compared to ages obtained from the radioactive disequilibria of 210Pb, in relation to its parent, 226Ra, in otolith cores of blackgill rockfish. Age estimates were validated up to 41 years, and a strong pattern of agreement supported a longevity exceeding 90 years. Age and length data fitted to the von Bertalanffy growth function indicated that blackgill rockfish are slow-growing (k= 0.040 females, 0.068 males) and that females grow slower than males, but reach a greater length. Age at 50% maturity, derived from previously published length-at-maturity estimates, was 17 years for males and 21 years for females. The results of this study agree with general life history traits already recognized for many Sebastes species, such as long life, slow growth, and late age at maturation. These traits may undermine the sustainability of blackgill rockfish populations when heavy fishing pressure, such as that which occurred in the 1980s, is applied.

Modeling red sea urchin (Strongylocentrotus franciscanus) growth using six growth functions

The growth of red sea urchins (Strongylocentrotus franciscanus) was modeled by using tag-recapture data from northern California. Red sea urchins (n=211) ranging in test diameter from 7 to 131 mm were examined for changes in size over one year. We used the function Jt+1 = Jt + f(Jt) to model growth, in which Jt is the jaw size (mm) at tagging, and Jt+1 is the jaw size one year later. The function f(Jt), represents one of six deterministic models: logistic dose response, Gaussian, Tanaka, Ricker, Richards, and von Bertalanffy with 3, 3, 3, 2, 3, and 2 minimization parameters, respectively. We found that three measures of goodness of fi t ranked the models similarly, in the order given. The results from these six models indicate that red sea urchins are slow growing animals (mean of 7.2 ±1.3 years to enter the fishery). We show that poor model selection or data from a limited range of urchin sizes (or both) produces erroneous growth parameter estimates and years-to-fishery estimates. Individual variation in growth dominated spatial variation at shallow and deep sites (F=0.246, n=199, P=0.62). We summarize the six models using a composite growth curve of jaw size, J, as a function of time, t: J = A(B – e–Ct) + Dt, in which each model is distinguished by the constants A, B, C, and D. We suggest that this composite model has the flexibility of the other six models and could be broadly applied. Given the robustness of our results regarding the number of years to enter the fishery, this information could be incorporated into future fishery management plans for red sea urchins in northern California.