Xylose isomerase from polycentric fungus Orpinomyces: gene sequencing, cloning, and expression in Saccharomyces cerevisiae for bioconversion of xylose to ethanol

The cDNA sequence of the gene for xylose isomerase from the rumen fungus Orpinomyces was elucidated by rapid amplification of cDNA ends. The 1,314-nucleotide gene was cloned and expressed constitutively in Saccharomyces cerevisiae. The deduced polypeptide sequence encoded a protein of 437 amino acids which showed the highest similarity to the family II xylose isomerases. Further, characterization revealed that the recombinant enzyme was a homodimer with a subunit of molecular mass 49 kDa. Cell extract of the recombinant strain exhibited high specific xylose isomerase activity. The pH optimum of the enzyme was 7.5, while the low temperature optimum at 37°C was the property that differed significantly from the majority of the reported thermophilic xylose isomerases. In addition to the xylose isomerase gene, the overexpression of the S. cerevisiae endogenous xylulokinase gene and the Pichia stipitis SUT1 gene for sugar transporter in the recombinant yeast facilitated the efficient production of ethanol from xylose.     

Environmental Profile of a Community's Health (EPOCH): an instrument to measure environmental determinants of cardiovascular health in five countries

BACKGROUND: The environment in which people live is known to be important in influencing diet, physical activity, smoking, psychosocial and other risk factors for cardiovascular (CV) disease. However no instrument exists that evaluates communities for these multiple environmental factors and is suitable for use across different communities, regions and countries. This report describes the design and reliability of an instrument to measure environmental determinants of CV risk factors. METHOD/PRINCIPAL FINDINGS: THE ENVIRONMENTAL PROFILE OF COMMUNITY HEALTH (EPOCH) INSTRUMENT COMPRISES TWO PARTS: (I) an assessment of the physical environment, and (II) an interviewer-administered questionnaire to collect residents' perceptions of their community. We examined the inter-rater reliability amongst 3 observers from each region of the direct observation component of the instrument (EPOCH I) in 93 rural and urban communities in 5 countries (Canada, Colombia, Brazil, China and India). Data collection using the EPOCH instrument was feasible in all communities. Reliability of the instrument was excellent (Intraclass Correlation Coefficient--ICC>0.75) for 24 of 38 items and fair to good (ICC 0.4-0.75) for 14 of 38 items. CONCLUSION: This report shows data collection with the EPOCH instrument is feasible and direct observation of community measures reliable. The EPOCH instrument will enable further research on environmental determinants of health for population studies from a broad range of settings.     

Regional distribution of wall thickness and failure properties of human abdominal aortic aneurysm

The regional distribution of wall thickness and failure properties in human abdominal aortic aneurysm (AAA) was explored. Three unruptured and one ruptured AAA were harvested as a whole during necropsy. Thickness was measured at about every 1.5 cm² wall surface area for an average of 100 measurement sites per AAA. Multiple longitudinally oriented rectangular specimen strips were cut at various locations from each AAA for a total of 48 strips. The strips were subjected to uniaxial extension until failure. Wall thickness varied regionally and between AAA from as low as 0.23 mm at a rupture site to 4.26 mm at a calcified site (median=1.48 mm). Wall thickness was slightly lower in the posterior and right regions. The failure tension (ultimate) of specimen strips varied regionally and between AAA from 5.5 N/cm close to a blister site in the ruptured AAA to 42.3 N/cm at the undilated neck of a 4 cm diameter unruptured AAA (median=14.8 N/cm). Failure stress (ultimate) varied from 33.6 to 235.1 N/cm² (median=126.6 N/cm²). There was no perceptible pattern in failure properties along the circumference. Failure tension of specimen strips at or close to blisters was mostly low. The rupture site in the ruptured aneurysm had the lowest recorded wall thickness of 0.23 mm with only slightly higher readings within a 1 cm radius. The failure tension of the specimen strip close to the rupture site was low (11.1 N/cm) compared to its neighborhood in the ruptured aneurysm.     

Involvement of p120 catenin in myopodial assembly and nerve–muscle synapse formation

At developing neuromuscular junctions (NMJs), muscles initially contact motor axons by microprocesses, or myopodia, which are induced by nerves and nerve‐secreted agrin, but it is unclear how myopodia are assembled and how they influence synaptic differentiation at the NMJ. Here, we report that treatment of cultured muscle cells with agrin transiently depleted p120 catenin (p120ctn) from cadherin junctions in situ, and increased the tyrosine phosphorylation and decreased the cadherin‐association of p120ctn in cell extracts. Whereas ectopic expression of wild‐type p120ctn in muscle generated myopodia in the absence of agrin, expression of a specific dominant‐negative mutant form of p120ctn, which blocks filopodial assembly in nonmuscle cells, suppressed nerve‐ and agrin‐induction of myopodia. Significantly, approaching neurites triggered reduced acetylcholine receptor (AChR) clustering along the edges of muscle cells expressing mutant p120ctn than of control cells, although the ability of the mutant cells to cluster AChRs was itself normal. Our results indicate a novel role of p120ctn in agrin‐induced myopodial assembly and suggest that myopodia increase muscle–nerve contacts and muscle's access to neural agrin to promote NMJ formation. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006     

FDG PET and MRI in Logopenic Primary Progressive Aphasia versus Dementia of the Alzheimer’s Type

Objectives

The logopenic variant of primary progressive aphasia is an atypical clinical variant of Alzheimer’s disease which is typically characterized by left temporoparietal atrophy on magnetic resonance imaging and hypometabolism on F-18 fluorodeoxyglucose positron emission tomography. We aimed to characterize and compare patterns of atrophy and hypometabolism in logopenic primary progressive aphasia, and determine which brain regions and imaging modality best differentiates logopenic primary progressive aphasia from typical dementia of the Alzheimer’s type.

Methods

A total of 27 logopenic primary progressive aphasia subjects underwent fluorodeoxyglucose positron emission tomography and volumetric magnetic resonance imaging. These subjects were matched to 27 controls and 27 subjects with dementia of the Alzheimer’s type. Patterns of atrophy and hypometabolism were assessed at the voxel and region-level using Statistical Parametric Mapping. Penalized logistic regression analysis was used to determine what combinations of regions best discriminate between groups.

Results

Atrophy and hypometabolism was observed in lateral temporoparietal and medial parietal lobes, left greater than right, and left frontal lobe in the logopenic group. The logopenic group showed greater left inferior, middle and superior lateral temporal atrophy (inferior p = 0.02; middle p = 0.007, superior p = 0.002) and hypometabolism (inferior p = 0.006, middle p = 0.002, superior p = 0.001), and less right medial temporal atrophy (p = 0.02) and hypometabolism (p<0.001), and right posterior cingulate hypometabolism (p<0.001) than dementia of the Alzheimer’s type. An age-adjusted penalized logistic model incorporating atrophy and hypometabolism achieved excellent discrimination (area under the receiver operator characteristic curve = 0.89) between logopenic and dementia of the Alzheimer’s type subjects, with optimal discrimination achieved using right medial temporal and posterior cingulate hypometabolism, left inferior, middle and superior temporal hypometabolism, and left superior temporal volume.

Conclusions

Patterns of atrophy and hypometabolism both differ between logopenic primary progressive aphasia and dementia of the Alzheimer’s type and both modalities provide excellent discrimination between groups.     

Ubiquitin‐dependent recruitment of the Bloom Syndrome helicase upon replication stress is required to suppress homologous recombination

Limiting the levels of homologous recombination (HR) that occur at sites of DNA damage is a major role of BLM helicase. However, very little is known about the mechanisms dictating its relocalization to these sites. Here, we demonstrate that the ubiquitin/SUMO‐dependent DNA damage response (UbS‐DDR), controlled by the E3 ligases RNF8/RNF168, triggers BLM recruitment to sites of replication fork stalling via ubiquitylation in the N‐terminal region of BLM and subsequent BLM binding to the ubiquitin‐interacting motifs of RAP80. Furthermore, we show that this mechanism of BLM relocalization is essential for BLM's ability to suppress excessive/uncontrolled HR at stalled replication forks. Unexpectedly, we also uncovered a requirement for RNF8‐dependent ubiquitylation of BLM and PML for maintaining the integrity of PML‐associated nuclear bodies and as a consequence the localization of BLM to these structures. Lastly, we identified a novel role for RAP80 in preventing proteasomal degradation of BLM in unstressed cells. Taken together, these data highlight an important biochemical link between the UbS‐DDR and BLM‐dependent pathways involved in maintaining genome stability.     

Differential induction of peroxidase and polyphenol oxidase isozymes in suspension-cultured cells of blast resistant and susceptible genotypes of rice in response to treatment with Magnaporthe grisea elicitor and toxin

The effect of elicitor from mycelial walls of Magnaporthe grisea, the rice blast fungus and α-picolinic acid, one of the toxins produced by M. grisea on induction of peroxidase (PO), polyphenol oxidase (PPO) in suspension-cultured rice (Oryza sativa L.) cells was studied. Cultured cells of blast resistant (Usen) and susceptible (CO39) rice genotypes were treated with elicitor (50?μg of glucose equivalents per ml) or α-picolinic acid (400?ppm). The cells were harvested at different time intervals and analysed for the induction of PO and PPO. PO isozyme analysis indicated that the elicitor strongly induced the activities of PO-2 and PO-3 in cultured cells of Usen 3?days after treatment. In Usen, toxin also induced the activities of PO-3 and PO-4. However, similar levels of activities corresponding to these isozymes were recorded 7?days after treatment. In CO39, the activities of PO-1 and PO-2 were induced 3?days after elicitor treatment. In contrast, the toxin suppressed the activity of PO-2. The elicitor induced the activities of PPO-1, PPO-2 and PPO-3 in both Usen and CO39. In Usen, steady increase of PPO-3 was observed and higher level of activity was recorded 5?days after treatment. In CO39, higher level of PPO-3 was observed 1?day after treatment and declined thereafter. However, the activities of PPO-1 and PPO-2 increased 3?days after treatment in CO39. In the toxin-treated cells of Usen, higher level of activity of PPO-3 was observed 3?days after treatment.     

Characterizing heterogeneous properties of cerebral aneurysms with unknown stress-free geometry: a precursor to in vivo identification

Knowledge of elastic properties of cerebral aneurysms is crucial for understanding the biomechanical behavior of the lesion. However, characterizing tissue properties using in vivo motion data presents a tremendous challenge. Aside from the limitation of data accuracy, a pressing issue is that the in vivo motion does not expose the stress-free geometry. This is compounded by the nonlinearity, anisotropy, and heterogeneity of the tissue behavior. This article introduces a method for identifying the heterogeneous properties of aneurysm wall tissue under unknown stress-free configuration. In the proposed approach, an accessible configuration is taken as the reference; the unknown stress-free configuration is represented locally by a metric tensor describing the prestrain from the stress-free configuration to the reference configuration. Material parameters are identified together with the metric tensor pointwisely. The paradigm is tested numerically using a forward-inverse analysis loop. An image-derived sac is considered. The aneurysm tissue is modeled as an eightply laminate whose constitutive behavior is described by an anisotropic hyperelastic strain-energy function containing four material parameters. The parameters are assumed to vary continuously in two assigned patterns to represent two types of material heterogeneity. Nine configurations between the diastolic and systolic pressures are generated by forward quasi-static finite element analyses. These configurations are fed to the inverse analysis to delineate the material parameters and the metric tensor. The recovered and the assigned distributions are in good agreement. A forward verification is conducted by comparing the displacement solutions obtained from the recovered and the assigned material parameters at a different pressure. The nodal displacements are found in excellent agreement.     

Micro and macroalgal biomass: A renewable source for bioethanol

Population outburst together with increased motorization has led to an overwhelming increase in the demand for fuel. In the milieu of economical and environmental concern, algae capable of accumulating high starch/cellulose can serve as an excellent alternative to food crops for bioethanol production, a green fuel for sustainable future. Certain species of algae can produce ethanol during dark-anaerobic fermentation and thus serve as a direct source for ethanol production. Of late, oleaginous microalgae generate high starch/cellulose biomass waste after oil extraction, which can be hydrolyzed to generate sugary syrup to be used as substrate for ethanol production. Macroalgae are also harnessed as renewable source of biomass intended for ethanol production. Currently there are very few studies on this issue, and intense research is required in future in this area for efficient utilization of algal biomass and their industrial wastes to produce environmentally friendly fuel bioethanol.