Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei

The filamentous fungus Trichoderma reesei has tremendous capability to secrete proteins. Therefore, it would be an excellent host for producing high levels of therapeutic proteins at low cost. Developing a filamentous fungus to produce sensitive therapeutic proteins requires that protease secretion is drastically reduced. We have identified 13 major secreted proteases that are related to degradation of therapeutic antibodies, interferon alpha 2b, and insulin like growth factor. The major proteases observed were aspartic, glutamic, subtilisin-like, and trypsin-like proteases. The seven most problematic proteases were sequentially removed from a strain to develop it for producing therapeutic proteins. After this the protease activity in the supernatant was dramatically reduced down to 4% of the original level based upon a casein substrate. When antibody was incubated in the six protease deletion strain supernatant, the heavy chain remained fully intact and no degradation products were observed. Interferon alpha 2b and insulin like growth factor were less stable in the same supernatant, but full length proteins remained when incubated overnight, in contrast to the original strain. As additional benefits, the multiple protease deletions have led to faster strain growth and higher levels of total protein in the culture supernatant.     

Qualitative and quantitative behavioral traits in a community of furcocercariae trematodes: tools for species separation?

Many trematode cercariae show distinct behavioral features, which have commonly been used in species identification in combination with morphological characteristics. However, information regarding cercariae behavior has often not been quantified in detail, or it is scattered in the literature, which is why the appropriate level of precision in behavioral identity, particularly in groups of cercariae species showing considerable morphological overlap, has not been properly established. In this study, we investigated one such group, the furcocercariae trematodes, by studying their behavior in a community consisting of 8 species (Diplostomum pseudospathaceum, Ichthyocotylurus variegatus, Cotylurus brevis, Cercaria spinulosa, Australapatemom sp., Australapatemom burti, Sanguinicola sp., and Bilharziella polonica) in central Finland. Our aim was not to develop an identification formula on the basis of behavior but to investigate and propose characteristic measurements applicable in separation of cercariae species. We used a 2-level approach, first recording qualitative behavioral traits of the cercariae, including swimming type and resting position; and, second, more detailed quantitative behavioral characteristics, such as resting time, swimming time, and swimming speed. Essentially, species showing a 2-phase behavior were distinguishable according to qualitative traits (resting position), whereas with those showing continuous swimming behavior, a combination of qualitative and quantitative traits (swimming speed) was required. These results suggest that characteristics of cercariae behavior can not only be used in species identification but also in general life history comparisons investigating details of the cercariae transmission.     

Work ability in midlife as a predictor of mortality and disability in later life: a 28-year prospective follow-up study

Background

Poor work ability correlates with increased morbidity and early retirement from the workforce, but the association in old age is not known. We investigated work ability in midlife among white-collar and blue-collar employees as a predictor of mortality and disability 28 years later.

Methods

A total of 5971 occupationally active people aged 44–58 years participated in the Finnish Longitudinal Study of Municipal Employees (FLAME) in 1981. Perceived work ability relative to lifetime best was categorized as excellent, moderate or poor. In 2009, the ability to perform activities of daily living was assessed among 2879 respondents (71.0% of the survivors). Mortality data were available up to July 2009.

Results

At the 28-year follow-up, 1918 of the 5971 participants had died and 1403 had some form of disability. Rates of death per 1000 person-years among white-collar men were 7.7 for those with excellent work ability, 14.7 for those with moderate work ability and 23.5 for those with poor work ability. Among blue-collar men, the corresponding rates were 15.5, 20.2 and 25.3. In women, rates ranged between 6.3 and 10.6 per 1000 person-years. The age-adjusted hazard ratios (HRs) for mortality were two to three times higher among blue-collar male employees with lower work ability than among white-collar male employees with excellent work ability in midlife (i.e., the reference group). The odds of death or disability at follow-up compared with white-collar workers with excellent work ability were highest among blue-collar employees with poor work ability in midlife (odds ratio [OR] 4.56, 95% confidence interval [CI] 2.82–7.37 for men; OR 3.37, 95% CI 2.28–4.98 for women). Among the survivors, similar but slightly lower risks of disability 28 years later were found.

Interpretation

Perceived poor work ability in midlife was associated with accelerated deterioration in health and functioning and remains evident after 28 years of follow-up.Prospective studies with a follow-up time stretching from midlife to old age have shown that lower socioeconomic status, as indicated by lower education level or occupational grade, predicts a decline in health and functioning in the working population.^1–4 This association is similar, if not more pronounced, in old age.^5–7Higher levels of work-related mental and physical strain increase the risk of early retirement and predict a decline in health and an increase in mortality among the working population.^3,8–15 However, the association between the demands of the work in conjunction with inadequate mental or physical resources (i.e., work ability)¹⁶ and health and functioning in old age has not been studied.¹⁷ Using a population-based 28-year follow-up study involving middle-aged municipal employees, we investigated whether work ability in midlife predicts the risk of death and disability during old age among white-collar and blue-collar employees.     

The screening of expression and purification conditions for replicative DNA polymerase associated B-subunits, assignment of the exonuclease activity to the C-terminus of archaeal pol D DP1 subunit

The B-subunits of replicative DNA polymerases belong to the superfamily of calcineurin-like phosphoesterases and are conserved from Archaea to humans. Recently we and others have shown that the B-subunit (DP1) of the archaeal family D DNA polymerase is responsible for proofreading 3'-5' exonuclease activity. The similarity of B-subunit sequences implies a common fold, but since the key catalytic and metal binding residues of the phosphoesterase domain are disrupted in the eukaryotic B-subunits, their common function has not been identified. To study the structure and activities of B-subunits in more detail, we expressed 13 different recombinant B-subunits in Escherichia coli. We found that the solubility of a protein could be predicted from the calculated GRAVY score. These scores were useful for the selection of proteins for successful expression. We optimized the expression and purification of Methanocaldococcus (Methanococcus) jannaschii DP1 of DNA polymerase D (MjaDP1) and show that the protein co-purifies with a thermostable nuclease activity. Truncation of the protein indicates that the N-terminus (aa 1-134) is not needed for catalysis. The C-terminal part of the protein containing both the calcineurin-like phosphoesterase domain and the OB-fold is sufficient for the nuclease activity.     

Mice with targeted disruption of spermidine/spermine N1-acetyltransferase gene maintain nearly normal tissue polyamine homeostasis but show signs of insulin resistance upon aging

The N(1)-acetylation of spermidine or spermine by spermidine/spermine N(1)-acetyltransferase (SSAT) is the ratecontrolling enzymatic step in the polyamine catabolism. We have now generated SSAT knockout (SSAT-KO) mice, which confirmed our earlier results with SSATdeficient embryonic stem (ES) cells showing only slightly affected polyamine homeostasis, mainly manifested as an elevated molar ratio of spermidine to spermine in most tissues indicating the indispensability of SSAT for the spermidine backconversion.Contrary to SSAT deficient ES cells, polyamine pools in SSAT-KO mice remained almost unchanged in response to N(1),N(11)-diethylnorspermine (DENSPM) treatment compared to a significant reduction of the polyamine pools in the wild-type animals and ES cells. Furthermore, SSATKO mice were more sensitive to the toxicity exerted by DENSPM in comparison with wild-type mice. The latter finding indicates that inducible SSAT plays an essential role in vivo in DENSPM treatmentevoked polyamine depletion, but a controversial role in toxicity of DENSPM. Surprisingly, liver polyamine pools were depleted similarly in wild-type and SSAT-KO mice in response to carbon tetrachloride treatment. Further characterization of SSAT knockout mice revealed insulin resistance at old age which supported the role of polyamine catabolism in glucose metabolism detected earlier with our SSAT overexpressing mice displaying enhanced basal metabolic rate, high insulin sensitivity and improved glucose tolerance. Therefore SSAT knockout mice might serve as a novel mouse model for type 2 diabetes.     

Factors affecting outdoor exposure in winter: population-based study

The extent of outdoor exposure during winter and factors affecting it were examined in a cross-sectional population study in Finland. Men and women aged 25–74 years from the National FINRISK 2002 sub-study (n=6,591) were queried about their average weekly occupational, leisure-time and total cold exposure during the past winter. The effects of gender, age, area of residence, occupation, ambient temperature, self-rated health, physical activity and education on cold exposure were analysed. The self-reported median total cold exposure time was 7 h/week (8 h men, 6 h women),<1 h/week (2 h men, 0 h women) at work, 4 h/week (5 h men, 4 h women) during leisure time and 1 h/week (1 h men, 1.5 h women) while commuting to work. Factors associated with increased occupational cold exposure among men were: being employed in agriculture, forestry and industry/mining/construction or related occupations, being less educated and being aged 55–64 years. Factors associated with increased leisure-time cold exposure among men were: employment in industry/mining/construction or related occupations, being a pensioner or unemployed, reporting at least average health, being physically active and having college or vocational education. Among women, being a housewife, pensioner or unemployed and engaged in physical activity increased leisure-time cold exposure, and young women were more exposed than older ones. Self-rated health was positively associated with leisure time cold exposure in men and only to a minor extent in women. In conclusion, the subjects reported spending 4% of their total time under cold exposure, most of it (71%) during leisure time. Both occupational and leisure-time cold exposure is greater among men than women.     

Genes involved in systemic and arterial bed dependent atherosclerosis--Tampere Vascular study

Background

Atherosclerosis is a complex disease with hundreds of genes influencing its progression. In addition, the phenotype of the disease varies significantly depending on the arterial bed.

Methodology/Principal Findings

We characterized the genes generally involved in human advanced atherosclerotic (AHA type V–VI) plaques in carotid and femoral arteries as well as aortas from 24 subjects of Tampere Vascular study and compared the results to non-atherosclerotic internal thoracic arteries (n=6) using genome-wide expression array and QRT-PCR. In addition we determined genes that were typical for each arterial plaque studied. To gain a comprehensive insight into the pathologic processes in the plaques we also analyzed pathways and gene sets dysregulated in this disease using gene set enrichment analysis (GSEA). According to the selection criteria used (>3.0 fold change and p-value <0.05), 235 genes were up-regulated and 68 genes down-regulated in the carotid plaques, 242 genes up-regulated and 116 down-regulated in the femoral plaques and 256 genes up-regulated and 49 genes down-regulated in the aortic plaques. Nine genes were found to be specifically induced predominantly in aortic plaques, e.g., lactoferrin, and three genes in femoral plaques, e.g., chondroadherin, whereas no gene was found to be specific for carotid plaques. In pathway analysis, a total of 28 pathways or gene sets were found to be significantly dysregulated in atherosclerotic plaques (false discovery rate [FDR] <0.25).

Conclusions

This study describes comprehensively the gene expression changes that generally prevail in human atherosclerotic plaques. In addition, site specific genes induced only in femoral or aortic plaques were found, reflecting that atherosclerotic process has unique features in different vascular beds.     

Retinotopic maps, spatial tuning, and locations of human visual areas in surface coordinates characterized with multifocal and blocked FMRI designs

The localization of visual areas in the human cortex is typically based on mapping the retinotopic organization with functional magnetic resonance imaging (fMRI). The most common approach is to encode the response phase for a slowly moving visual stimulus and to present the result on an individual's reconstructed cortical surface. The main aims of this study were to develop complementary general linear model (GLM)-based retinotopic mapping methods and to characterize the inter-individual variability of the visual area positions on the cortical surface. We studied 15 subjects with two methods: a 24-region multifocal checkerboard stimulus and a blocked presentation of object stimuli at different visual field locations. The retinotopic maps were based on weighted averaging of the GLM parameter estimates for the stimulus regions. In addition to localizing visual areas, both methods could be used to localize multiple retinotopic regions-of-interest. The two methods yielded consistent retinotopic maps in the visual areas V1, V2, V3, hV4, and V3AB. In the higher-level areas IPS0, VO1, LO1, LO2, TO1, and TO2, retinotopy could only be mapped with the blocked stimulus presentation. The gradual widening of spatial tuning and an increase in the responses to stimuli in the ipsilateral visual field along the hierarchy of visual areas likely reflected the increase in the average receptive field size. Finally, after registration to Freesurfer's surface-based atlas of the human cerebral cortex, we calculated the mean and variability of the visual area positions in the spherical surface-based coordinate system and generated probability maps of the visual areas on the average cortical surface. The inter-individual variability in the area locations decreased when the midpoints were calculated along the spherical cortical surface compared with volumetric coordinates. These results can facilitate both analysis of individual functional anatomy and comparisons of visual cortex topology across studies.