Functional Analysis of the Genes Encoding Diaminopropionate Ammonia Lyase in Escherichia coli and Salmonella enterica Serovar Typhimurium

Diaminopropionate ammonia lyase (DAPAL) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the conversion of diaminopropionate (DAP) to pyruvate and ammonia and plays an important role in cell metabolism. We have investigated the role of the ygeX gene of Escherichia coli K-12 and its ortholog, STM1002, in Salmonella enterica serovar Typhimurium LT2, presumed to encode DAPAL, in the growth kinetics of the bacteria. While Salmonella Typhimurium LT2 could grow on DL-DAP as a sole carbon source, the wild-type E. coli K-12 strain exhibited only marginal growth on DL-DAP, suggesting that DAPAL is functional in S. Typhimurium. The expression of ygeX in E. coli was low as detected by reverse transcriptase PCR (RT-PCR), consistent with the poor growth of E. coli on DL-DAP. Strains of S. Typhimurium and E. coli with STM1002 and ygeX, respectively, deleted showed loss of growth on DL-DAP, confirming that STM1002 (ygeX) is the locus encoding DAPAL. Interestingly, the presence of DL-DAP caused a growth inhibition of the wild-type E. coli strain as well as the knockout strains of S. Typhimurium and E. coli in minimal glucose/glycerol medium. Inhibition by DL-DAP was rescued by transforming the strains with plasmids containing the STM1002 (ygeX) gene encoding DAPAL or supplementing the medium with Casamino Acids. Growth restoration studies using media lacking specific amino acid supplements suggested that growth inhibition by DL-DAP in the absence of DAPAL is associated with auxotrophy related to the inhibition of the enzymes involved in the biosynthetic pathways of pyruvate and aspartate and the amino acids derived from them.

Deformation and Recrystallization texture evolution in Nano-crystalline Nickel

Deformation and recrystallization textures in nano-crystalline nickel with average grain size of 20 nm were investigated using X-ray diffraction, electron microscopy and differential scanning calorimetry. The deformation behaviour of nano-crystalline nickel is quite complicated due to intervention of other deformation mechanisms like grain boundary sliding and restoration mechanisms like grain growth and grain rotation to dislocation mediated slip. Recrystallization studies carried out on the deformed nano-crystalline nickel showed that the deformation texture was retained during low temperature annealing (300 degrees C), while at higher temperature (1000 degrees C), the texture got randomised. The exact mechanism of texture formation during deformation and recrystallization has been discussed.

Oncogenic MicroRNA-155 Down-regulates Tumor Suppressor CDC73 and Promotes Oral Squamous Cell Carcinoma Cell Proliferation IMPLICATIONS FOR CANCER THERAPEUTICS

The CDC73 gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. It negatively regulates beta-catenin, cyclin D1, and c-MYC. Down-regulation of CDC73 has been reported in breast, renal, and gastric carcinomas. However, the reports regarding the role of CDC73 in oral squamous cell carcinoma (OSCC) are lacking. In this study we show that CDC73 is down-regulated in a majority of OSCC samples. We further show that oncogenic microRNA-155 (miR-155) negatively regulates CDC73 expression. Our experiments show that the dramatic up-regulation of miR-155 is an exclusive mechanism for down-regulation of CDC73 in a panel of human cell lines and a subset of OSCC patient samples in the absence of loss of heterozygosity, mutations, and promoter methylation. Ectopic expression of miR-155 in HEK293 cells dramatically reduced CDC73 levels, enhanced cell viability, and decreased apoptosis. Conversely, the delivery of a miR-155 antagonist (antagomir-155) to KB cells overexpressing miR-155 resulted in increased CDC73 levels, decreased cell viability, increased apoptosis, and marked regression of xenografts in nude mice. Cotransfection of miR-155 with CDC73 in HEK293 cells abrogated its pro-oncogenic effect. Reduced cell proliferation and increased apoptosis of KB cells were dependent on the presence or absence of the 3'-UTR in CDC73. In summary, knockdown of CDC73 expression due to overexpression of miR-155 not only adds a novelty to the list of mechanisms responsible for its down-regulation in different tumors, but the restoration of CDC73 levels by the use of antagomir-155 may also have an important role in therapeutic intervention of cancers, including OSCC.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

Water treatment potential in relation to phytoplankton dynamics in tropical sewage-fed urban water bodies

Urban water bodies frequently receive untreated sewage and water levels in such water bodies are maintained by daily inputs of sewage. They function as “variable-zone” anaerobic-aerobic lagoons suffering several macrophyte, biotic and abiotic stresses. We have studied two such lakes in Bangalore (Bellandur-360 ha and Varthur-220 ha) to understand whether such an occurrence could be made beneficial (maintaining water levels as well as treatment). Such hypertrophic water body receives sewage at 180-250mg/L and is discharged at 25-80mg/L COD/BOD in different seasons. In an earlier study we reported macrophyte altering the purification function of the water body. In this paper we studied the impact of phytoplankton dynamics and macrophyte cover on the functions such as organic load removal. Algal community analysis, algal biomass, macrophyte cover, water quality, nutrient status was studied seasonally during 2009-2010. Oxygen deficiency and sometimes anoxia, recorded from surface samples resulted in high quantities of NH4+-N (30-40mg/L) and phosphate (0.5-4mg/L)-characteristics of anoxic hypertrophic urban lakes. The productiveness favoured high phytoplanktonic community characterized by small cells (<10μm; Chlorella sp. - highest numbers). The lake could be clearly demarcated into an initial anaerobic zone (40% area), a facultative zone (20%) and an aerobic zone (40%) based on redox values and GIS/bathymetry. During summer the lake is covered by floating macrophytes converting the lake into an anoxic/anaerobic water pool subduing the water purification function as well as aesthetics. When macrophytes are controlled such sewage fed water bodies can be used for treating urban wastewater while also maintaining water sustainability in these semi-arid ecosystems. This paper reports the community dynamics of phytoplankton, their function and competition with macrophytes.

Effects of different modes of hot cross-rolling in 7010 aluminum alloy: part I. evolution of microstructure and texture

The current study describes the evolution of microstructure and texture in an Al-Zn-Mg-Cu-Zr-based 7010 aluminum alloy during different modes of hot cross-rolling. Processing of materials involves three different types of cross-rolling. The development of texture in the one-step cross-rolled specimen can be described by a typical beta-fiber having the maximum intensity near Copper (Cu) component. However, for the multi-step cross-rolled specimens, the as-rolled texture is mainly characterized by a strong rotated-Brass (Bs) component and a very weak rotated-cube component. Subsequent heat treatment leads to sharpening of the major texture component (i.e., rotated-Bs). Furthermore, the main texture components in all the specimens appear to be significantly rotated in a complex manner away from their ideal positions because of non-symmetric deformations in the two rolling directions. Detailed microstructural study indicates that dynamic recovery is the dominant restoration mechanism operating during the hot rolling. During subsequent heat treatment, static recovery dominates, while a combination of particle-stimulated nucleation (PSN) and strain-induced grain boundary migration (SIBM) causes partial recrystallization of the grain structure. The aforementioned restoration mechanisms play an important role in the development of texture components. The textural development in the current study could be attributed to the combined effects of (a) cross-rolling and inter-pass annealing that reduce the intensity of Cu component after each successive pass, (b) recrystallization resistance of Bs-oriented grains, (c) stability of Bs texture under cross-rolling, and (d) Zener pinning by Al3Zr dispersoids.

Evolution of microstructure and texture in friction stir processed Al-Mg-Mn alloy

Friction stir processing was carried out on the Al-Mg-Mn alloy to achieve ultrafine grained microstructure. The evolution of microstructure and micro-texture was studied in different regions of the deformed sample, namely nugget zone, thermo-mechanically affected zone (TMAZ) and base metal. The average grain sizes of the nugget zone, TMAZ and base metal are 1.5 mu m +/- 0.5 mu m, 15 mu m +/- 8 mu m, and 80 mu m +/- 10 mu m, respectively. The TMAZ exhibits excessive deformation banding structure and sub-grain formation. The orientation gradient within the sub-grain is dependent on grain size, orientation, and distance from nugget zone. The microstructure was partitioned based on the grain orientation spread and grain size values to separate the recrystallized fraction from the deformed region in order to understand the micromechanism of grain refinement. The texture of both deformed and recrystallized regions are similar in nature. Microstructure and texture analysis suggest that the restoration processes are different in different regions of the processed sample. The transition region between nugget zone and TMAZ exhibits large elongated grains surrounded by fine equiaxed grains of different orientation which indicate the process of discontinuous dynamic recrystallization. Within the nugget zone, similar texture between deformed and recrystallized grain fraction suggests that the restoration mechanism is a continuous process.

MPK-09, a small molecule inspired from bioactive styryllactone restores the wild-type function of mutant p53

In the search for more efficacious and less toxic cancer drugs, the tumor suppressor p53 protein has long been a desirable therapeutic target. In the recent past, few independent studies have demonstrated that the antitumor activity of wild-type p53 can be restored in cancer cells harboring mutant form of p53 using small molecule activators. In this study, we describe a novel small molecule MPK-09, which is selective and highly potent against allele specific p53 mutations mainly, R175H, R249S, R273H, R273C, and E285K. Except E285K, all other mutations tested are among the six ``hot spot'' p53 mutations reported in majority of human cancer. Furthermore, our study conclusively demonstrates that the apoptotic activity of the small molecule MPK-09 against cancer cells harboring R273C and E285K mutations is due to restoration of the wild-type conformation to the corresponding mutant form of p53.

Assessing resilience and state-transition models with historical records of cheatgrass Bromus tectorum invasion in North American sagebrush-steppe

1. Resilience-based approaches are increasingly being called upon to inform ecosystem management, particularly in arid and semi-arid regions. This requires management frameworks that can assess ecosystem dynamics, both within and between alternative states, at relevant time scales. 2. We analysed long-term vegetation records from two representative sites in the North American sagebrush-steppe ecosystem, spanning nine decades, to determine if empirical patterns were consistent with resilience theory, and to determine if cheatgrass Bromus tectorum invasion led to thresholds as currently envisioned by expert-based state-and-transition models (STM). These data span the entire history of cheatgrass invasion at these sites and provide a unique opportunity to assess the impacts of biotic invasion on ecosystem resilience. 3. We used univariate and multivariate statistical tools to identify unique plant communities and document the magnitude, frequency and directionality of community transitions through time. Community transitions were characterized by 37-47% dissimilarity in species composition, they were not evenly distributed through time, their frequency was not correlated with precipitation, and they could not be readily attributed to fire or grazing. Instead, at both sites, the majority of community transitions occurred within an 8-10year period of increasing cheatgrass density, became infrequent after cheatgrass density peaked, and thereafter transition frequency declined. 4. Greater cheatgrass density, replacement of native species and indication of asymmetry in community transitions suggest that thresholds may have been exceeded in response to cheatgrass invasion at one site (more arid), but not at the other site (less arid). Asymmetry in the direction of community transitions also identified communities that were at-risk' of cheatgrass invasion, as well as potential restoration pathways for recovery of pre-invasion states. 5. Synthesis and applications. These results illustrate the complexities associated with threshold identification, and indicate that criteria describing the frequency, magnitude, directionality and temporal scale of community transitions may provide greater insight into resilience theory and its application for ecosystem management. These criteria are likely to vary across biogeographic regions that are susceptible to cheatgrass invasion, and necessitate more in-depth assessments of thresholds and alternative states, than currently available.

X-ray diffraction and Mossbauer spectroscopy studies of cementite dissolution in cold-drawn pearlitic steel

Cementite dissolution in cold-drawn pearlitic steel (0.8 wt.% carbon) wires has been studied by quantitative X-ray diffraction (XRD) and Mossbauer spectroscopy up to drawing strain 1.4. Quantification of cementite-phase fraction by Rietveld analysis has confirmed more than 50% dissolution of cementite phase at drawing strain 1.4. It is found that the lattice parameter of the ferrite phase determined by Rietveld refinement procedure remains nearly unchanged even after cementite dissolution. This confirms that the carbon atoms released after cementite dissolution do not dissolve in the ferrite lattice as Fe-C interstitial solid solution. Detailed analysis of broadening of XRD line profiles for the ferrite phase shows high density of dislocations (approximate to 10(15)/m(2)) in the ferrite matrix at drawing strain 1.4. The results suggest a dominant role of 111 screw dislocations in the cementite dissolution process. Post-deformation heat treatment leads to partial annihilation of dislocations and restoration of cementite phase. Based on these experimental observations, further supplemented by TEM studies, we have suggested an alternative thermodynamic mechanism of the dissolution process.

Spatially Adaptive Kernel Regression Using Risk Estimation

An important question in kernel regression is one of estimating the order and bandwidth parameters from available noisy data. We propose to solve the problem within a risk estimation framework. Considering an independent and identically distributed (i.i.d.) Gaussian observations model, we use Stein's unbiased risk estimator (SURE) to estimate a weighted mean-square error (MSE) risk, and optimize it with respect to the order and bandwidth parameters. The two parameters are thus spatially adapted in such a manner that noise smoothing and fine structure preservation are simultaneously achieved. On the application side, we consider the problem of image restoration from uniform/non-uniform data, and show that the SURE approach to spatially adaptive kernel regression results in better quality estimation compared with its spatially non-adaptive counterparts. The denoising results obtained are comparable to those obtained using other state-of-the-art techniques, and in some scenarios, superior.

Role of the loop L-4,L-5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation

Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L-4,L-5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L-4,L-5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L-4,L-5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein-bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.

Vermicompost reduces the invasiveness of the earthworm species Dichogaster bolaui compared to the use of compost in a degraded tropical soil in Northern Vietnam

In Northern Vietnam, organic fertilization programmes are being tested to restore soil fertility and reduce soil erosion. However, the amendment of organic matter in soil is also associated with the development of the invasive earthworm species Dichogaster bolaui. The objective of this study was to investigate the influence of organic matter amendment quality (compost vs. vermicompost) on D. bolaui. Our study confirmed D. bolaui development in organic patches in the field. However, we also observed that the flat-backed millipede Asiomorpha coarctata proliferated in these organic patches. Native to Asia, this millipede species is also considered as invasive in America. Both D. bolaui and A. coarctata more rapidly colonized compost than vermicompost patches. A laboratory experiment confirmed this trend and showed the limited development of D. bolaui in vermicompost. This is probably because of the decreased palatability of this substrate to soil fauna. In conclusion, any restoration practice that aims to increase the organic stocks in soils degraded by erosion should consider the quality of the organic amendment. In Northern Vietnam, vermicompost may be the preferred substrate for restoring soils while limiting the spread of D. bolaui. (C) 2014 Elsevier Masson SAS. All rights reserved.

Impacts of climate change and management responses in tropical forests depend on complex frugivore-mediated seed dispersal

AimBiodiversity outcomes under global change will be influenced by a range of ecological processes, and these processes are increasingly being considered in models of biodiversity change. However, the level of model complexity required to adequately account for important ecological processes often remains unclear. Here we assess how considering realistically complex frugivore-mediated seed dispersal influences the projected climate change outcomes for plant diversity in the Australian Wet Tropics (all 4313 species). LocationThe Australian Wet Tropics, Queensland, Australia. MethodsWe applied a metacommunity model (M-SET) to project biodiversity outcomes using seed dispersal models that varied in complexity, combined with alternative climate change scenarios and habitat restoration scenarios. ResultsWe found that the complexity of the dispersal model had a larger effect on projected biodiversity outcomes than did dramatically different climate change scenarios. Applying a simple dispersal model that ignored spatial, temporal and taxonomic variation due to frugivore-mediated seed dispersal underestimated the reduction in the area of occurrence of plant species under climate change and overestimated the loss of diversity in fragmented tropical forest remnants. The complexity of the dispersal model also changed the habitat restoration approach identified as the best for promoting persistence of biodiversity under climate change. Main conclusionsThe consideration of complex processes such as frugivore-mediated seed dispersal can make an important difference in how we understand and respond to the influence of climate change on biodiversity.

Stable isotope evidence for ca. 2.7-Ga-old Archean cap carbonates from the Dharwar Supergroup, southern India

Carbon isotope compositions of carbonate rocks from similar to 2.7-Ga-old Neoarchean Vanivilas Formation of the Dharwar Supergroup presented earlier by us are re-evaluated in this study, besides oxygen isotope compositions of a few silica dolomite pairs. The purpose of such a revisit assumes significance in view of recent field evidences that suggest a glaciomarine origin for the matrix-supported conglomerate member, the Talya conglomerate, which underlies the carbonate rocks of the Vanivilas Formation. An in-depth analysis of carbon isotope data reveals preservation of their pristine character despite the rocks having been subjected to metamorphism to different degrees (from lower greenschist to lower amphibolite facies). The dolomitic member of Vanivilas Formation of Marikanive area is characterized by highly depleted delta C-13 value (up to -5 parts per thousand VPDB) and merits as the Indian example of ca. 2.7-Ga-old cap carbonate. This inference is further supported by estimated low temperature of equilibration documented by a few silica dolomite pairs from the Vanivilas Formation collected near Kalche area. These pairs show evidence for oxygen isotopic equilibrium at low temperatures (similar to 0-20 degrees C) with depleted water (delta O-18 = -21 parts per thousand to -15 parts per thousand VSMOW) of glacial origin. We propose that the mineral pairs were deposited during the deglaciation period when the ocean temperature was in its gradual restoration phase. The dolomite of Marikanive area is the first record of cap carbonates from the Indian subcontinent with Neoarchean antiquity.