The HOME microscope workstation. A new tool for cervical cancer screening.

The Highly Optimized Microscope Environment (HOME) is a computerized microscope design for assisting pathologists and cytotechnologists in routine clinical tasks. The prototype system consists of an IBM PC-compatible computer and a light microscope in which a built-in high-resolution computer display image is super-imposed on the optical image of the specimen. Also, an encoding stage and objective turret encoder are used to provide continuous monitoring of the stage coordinates and microscope magnification to the computer. This allows any position on the stage to be uniquely defined. Software, written in C language and running under the MS-DOS/MS-Windows environment, is controlled by means of a mouse-driven cursor. A specific application has been developed for cervical cancer screening, taking into account the needs and constraints of microscopists performing this task. Informatics tools offered by the HOME system provide them with precise flagging and relocation of objects on the slide, control of the scanning pathway, and ability to write and print the report directly through the microscope. The computer files generated by microscopic examination are stored and contain information available for quality control assessment and laboratory management.     

Evolutionary dynamics and highly optimized tolerance

We develop a numerical model of a lattice community based on Highly Optimized Tolerance (HOT), which relates the evolution of complexity to robustness tradeoffs in an uncertain environment. With the model, we explore scenarios for evolution and extinction which are abstractions of processes which are commonly discussed in biological and ecological case studies. These include the effects of different habitats on the phenotypic traits of the organisms, the effects of different mutation rates on adaptation, fitness, and diversity, and competition between generalists and specialists. The model exhibits a wide variety of microevolutionary and macroevolutionary phenomena which can arise in organisms which are subject to random mutation, and selection based on fitness evaluated in a specific environment. Generalists arise in uniform habitats, where different disturbances occur with equal frequency, while specialists arise when the relative frequency of different disturbances is skewed. Fast mutators are seen to play a primary role in adaptation, while slow mutators preserve well-adapted configurations. When uniform and skewed habitats are coupled through migration of the organisms, we observe a primitive form of punctuated equilibrium. Rare events in the skewed habitat lead to extinction of the specialists, whereupon generalists invade from the uniform habitat, adapt to their new surroundings, ultimately leading their progeny to become vulnerable to extinction in a subsequent rare disturbance.     

Global photosynthetic capacity is optimized to the environment

Earth system models (ESMs) use photosynthetic capacity, indexed by the maximum Rubisco carboxylation rate (V_cmax), to simulate carbon assimilation and typically rely on empirical estimates, including an assumed dependence on leaf nitrogen determined from soil fertility. In contrast, new theory, based on biochemical coordination and co‐optimization of carboxylation and water costs for photosynthesis, suggests that optimal V_cmax can be predicted from climate alone, irrespective of soil fertility. Here, we develop this theory and find it captures 64% of observed variability in a global, field‐measured V_cmax dataset for C₃ plants. Soil fertility indices explained substantially less variation (32%). These results indicate that environmentally regulated biophysical constraints and light availability are the first‐order drivers of global photosynthetic capacity. Through acclimation and adaptation, plants efficiently utilize resources at the leaf level, thus maximizing potential resource use for growth and reproduction. Our theory offers a robust strategy for dynamically predicting photosynthetic capacity in ESMs.     

Light-activation of NADP-malate dehydrogenase: A highly controlled process for an optimized function

The chloroplastic nicotinamide adenine dinucleotide phosphate-malate dehydrogenase (NADP-MDH) (EC 1.1.1.82), a key enzyme of photosynthetic carbon assimilation of the C4 NADP-malic enzyme type plants, is strictly regulated by light through the ferredoxin-thioredoxin system. It is inactive in the dark, in the oxidized form, and activated in the light by the reduction of specific regulatory disulfides. A site-directed mutagenesis approach allowed localization of the regulatory disulfides in the N- and C-terminal sequence extensions conserved in all the light-regulated chloroplastic malate dehydrogenases. These extensions do not exist in the permanently active NAD-dependent MDHs (EC 1.1.1.37). Biochemical characterization of the mutants and elimination of negative charges at the C-terminus provided evidence for auto-inhibition of the oxidized enzyme by its C-terminal end through interaction with the active site and showed that the more compact structure of the oxidized dimer was linked to the presence of the N-terminal disulfide. The recently published 3-dimensional structures of the oxidized enzyme confirmed the location of the regulatory disulfides and fully support the auto-inhibition hypothesis. Indeed, the C-terminus is trapped inside the active site, interacting with active-site residues, and the N-termini are inserted at the dimer contact area where they are bound by hydrophobic interactions with both subunits. The physiological function of such complex regulation is discussed.     

In-vitro selection of highly stabilized protein variants with optimized surface

Thermostable proteins are of prime importance in protein science, but it has remained difficult to develop general strategies for stabilizing a protein. Site-directed mutagenesis based on comparisons with thermophilic homologs is rarely successful because the sequence differences are too numerous and dominated by neutral mutations. Here we used a method of directed evolution to increase the stability of a mesophilic protein, the cold shock protein Bs-CspB from Bacillus subtilis. It differs from its thermophilic counterpart Bc-Csp from Bacillus caldolyticus at 12 surface-exposed positions. To elucidate the stabilizing potential of exposed amino acid residues, six of these variant positions were randomized by saturation mutagenesis, the corresponding library of sequences was inserted into the gene-3-protein of the filamentous phage fd, and stabilized variants were selected by the Proside technique. Proside links the increased protease resistance of stabilized protein variants with the infectivity of the phage. Many strongly stabilized variants of Bs-CspB were identified in two selections, one in the presence of a denaturant and the other at elevated temperature. Several of them are significantly more stable than the naturally thermostable homolog Bc-Csp, and the best variant reaches Tm-Csp (the homolog from the hyperthermophile Thermotoga maritima) in stability. Remarkably, this variant differs from Tm-Csp at five and from Bc-Csp at all six randomized positions. This indicates that proteins can be strongly stabilized by many different sets of surface mutations, and Proside selects them efficiently from large libraries. The course of the selection could be directed by the conditions. In an ionic denaturant non-polar surface interactions were optimized, whereas at elevated temperature variants with improved electrostatics were selected, pointing to two different strategies for stabilization at protein surfaces.     

Paraneuronal pseudobranchial neurosecretory cells in scorpion catfish Heteropneustes fossilis: an environment scanning electron microscope and transmission electron microscope study

Yadav, L., Sengar, M., Zaccone, D. and Gopesh, A. 2011. Paraneuronal pseudobranchial neurosecretory cells in scorpion catfish Heteropneustes fossilis: an environment scanning electron microscope and transmission electron microscope study. —Acta Zoologica (Stockholm) 00 : 1–8. Pseudobranchial neurosecretory system (PNS), found in the gill region of certain groups of teleosts, falls under the category of the ‘diffuse neuroendocrine system’ (DNES). The cells belonging to the system share morpho‐functional features with the paraneuronal cells observed in respiratory tract and airway surfaces of higher vertebrates. On the basis of the experimental observations, a role in condition of hypoxia has been recorded for this system. In an attempt to elucidate the ultrastructure of pseudobranchial neurosecretory cells, present investigation was undertaken using environment scanning electron microscope (ESEM) and TEM in an air‐breathing catfish, Heteropneustes fossilis. The external morphology of PNS under ESEM appeared as a mass of cells supplied with nerves and blood capillaries. Each cell mass is made up of numerous pear‐shaped neurosecretory cells, confirmed by neurosecretion‐specific acid violet stain. The TEM investigation of the cells revealed the presence of different sizes of dense‐cored vesicles in the cytoplasm, which was observed as granular cytoplasm under light microscope. Presence of large number of mitochondria in the cytoplasm confirmed active involvement of these cells in the physiology of fishes. Although lacuna prevails regarding the exact function of this system of fish, its probable role in hypoxic condition and surfacing behavior are speculated.     

OPSA: an optimized prediction based scheduling approach for scientific applications in cloud environment

Cluster Computing - Cloud computing has attracted scientists to deploy scientific applications by offering services such as Infrastructure-as-a-service (IaaS), Software-as-a-service (SaaS), and...     

In vitro selection of RNase P RNA reveals optimized catalytic activity in a highly conserved structural domain.

In vitro selection techniques are useful means of dissecting the functions of both natural and artificial ribozymes. Using a self-cleaving conjugate containing the Escherichia coli ribonuclease P RNA and its substrate, pre-tRNA (Frank DN, Harris ME, Pace NR, 1994, Biochemistry 33:10800-10808), we have devised a method to select for catalytically active variants of the RNase P ribozyme. A selection experiment was performed to probe the structural and sequence constraints that operate on a highly conserved region of RNase P: the J3/4-P4-J2/4 region, which lies within the core of RNase P and is thought to bind catalytically essential magnesium ions (Harris ME et al., 1994, EMBO J 13:3953-3963; Hardt WD et al., 1995, EMBO J 14:2935-2944; Harris ME, Pace NR, 1995, RNA 1:210-218). We sought to determine which, if any, of the nearly invariant nucleotides within J3/4-P4-J2/4 are required for ribozyme-mediated catalysis. Twenty-two residues in the J3/4-P4-J2/4 component of RNase P RNA were randomized and, surprisingly, after only 10 generations, each of the randomized positions returned to the wild-type sequence. This indicates that every position in J3/4-P4-J2/4 contributes to optimal catalytic activity. These results contrast sharply with selections involving other large ribozymes, which evolve improved catalytic function readily in vitro (Chapman KB, Szostak JW, 1994, Curr Opin Struct Biol 4:618-622; Joyce GF, 1994, Curr Opin Struct Biol 4:331-336; Kumar PKR, Ellington AE, 1995, FASEB J 9:1183-1195). The phylogenetic conservation of J3/4-P4-J2/4, coupled with the results reported here, suggests that the contribution of this structure to RNA-mediated catalysis was optimized very early in evolution, before the last common ancestor of all life.     

Prevalence of highly host-specific cyanophages in the estuarine environment

Cyanophages that infect coastal and oceanic Synechococcus have been studied extensively. However, no cyanophages infecting estuarine Synechococcus have been reported. In this study, seven cyanophages (three podoviruses, three siphoviruses and one myovirus) isolated from four estuarine Synechococcus strains were characterized in terms of their morphology, host range, growth and genetic features. All the podoviruses and siphoviruses were highly host specific. For the first time, the photosynthesis gene ( psbA ) was found in two podoviruses infecting estuarine Synechococcus . However, the psbA gene was not detected in the three siphoviruses. The psbA sequences from the two Synechococcus podoviruses clustered with some environmental psbA sequences, forming a unique cluster distantly related to previous known psbA clusters. Our results suggest that the psbA among Synechococcus podoviruses may evolve independently from the psbA of Synechococcus myoviruses. All three estuarine Synechococcus podoviruses contained the DNA polymerase ( pol ) gene, and clustered with other podoviruses that infect oceanic Synechococcus and Prochlorococcus , suggesting that the DNA pol is conserved among marine picocyanobacterial podoviruses. Prevalence of host-specific cyanophages in the estuary suggests that Synechococcus and their phages in the estuarine ecosystem may develop a host–phage relationship different from what have been found in the open ocean.