Correlation of gene expression and protein production rate - a system wide study

<p>Abstract</p> <p>Background</p> <p>Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on <it>Saccharomyces cerevisiae </it>chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus <it>Trichoderma reesei </it>(<it>Hypocrea jecorina</it>) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype.</p> <p>Results</p> <p>We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of <it>T. reesei</it>. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response.</p> <p>Conclusions</p> <p>Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).</p

Animal models for aberrations of gonadotropin action

During the last two decades a large number of genetically modified mouse lines with altered gonadotropin action have been generated. These mouse lines fall into three categories: the lack-of-function mice, gain-of-function mice, and the mice generated by breeding the abovementioned lines with other disease model lines. The mouse strains lacking gonadotropin action have elucidated the necessity of the pituitary hormones in pubertal development and function of gonads, and revealed the processes from the original genetic defect to the pathological phenotype such as hypo- or hypergonadotropic hypogonadism. Conversely, the strains of the second group depict consequences of chronic gonadotropin action. The lines vary from those expressing constitutively active receptors and those secreting follicle-stimulating hormone (FSH) with slowly increasing amounts to those producing human choriogonadotropin (hCG), amount of which corresponds to 2000-fold luteinizing hormone (LH)/hCG biological activity. Accordingly, the phenotypes diverge from mild anomalies and enhanced fertility to disrupted gametogenesis, but eventually chronic, enhanced and non-pulsatile action of both FSH and LH leads to female and male infertility and/or hyper- and neoplasias in most of the gonadotropin gain-of-function mice. Elevated gonadotropin levels also alter the function of several extra-gonadal tissues either directly or indirectly via increased sex steroid production. These effects include promotion of tumorigenesis in tissues such as the pituitary, mammary and adrenal glands. Finally, the crossbreedings of the current mouse strains with other disease models are likely to uncover the contribution of gonadotropins in novel biological systems, as exemplified by the recent crossbreed of LHCG receptor deficient mice with Alzheimer disease mice

Analyzing Measurement Invariance of the Students’ Engagement Instrument Brief Version : The Cases of Denmark, Finland, and Portugal

The promotion of students’ engagement with school is an internationally acknowledged challenge in education. There is a need to examine the structure of the concept of student engagement and to discover the best practices for fostering it across societies. That is why the cross-cultural invariance testing of students’ engagement measures is highly needed. This study aimed, first, to find the reduced set of theoretically valid items to represent students’ affective and cognitive engagement forming the Brief-SEI (brief version of the Student Engagement Instrument; SEI). The second aim was to test the measurement invariance of the Brief-SEI across three countries (Denmark, Finland, and Portugal). A total of 4,437 seventh-grade students completed the SEI questionnaires in the three countries. The analyses revealed that of the total 33 original instrument items, 15 items indicated acceptable psychometric properties of the Brief-SEI. With these 15 items, cross-national factorial validity and invariances across genders and students with different levels of academic performance (samples from Finland and Portugal) were demonstrated. This article discusses the utility of the Brief-SEI in cross-cultural research and its applicability in different national school contexts.peerReviewe

Models for supercritical motion in a superfluid Fermi liquid

Abstract We study the drag force on objects moving in a Fermi superfluid at velocities on the order of the Landau velocity vL. The expectation has been that vL is the critical velocity beyond which the drag force starts to increase toward its normal-state value. This expectation is challenged by a recent experiment measuring the heat generated by a uniformly moving wire immersed in superfluid ³He. We introduce the basis for the calculation of the drag force on a macroscopic object using the Fermi-liquid theory of superfluidity. As a technical tool in the calculations, we propose a boundary condition that describes diffuse reflection of quasiparticles from a surface on a scale that is larger than the superfluid coherence length. We calculate the drag force on steadily moving objects of different sizes. For an object that is small compared to the coherence length, we find a drag force that is in accordance with the expectation. For a macroscopic object, we need to take into account the spatially varying flow field around the object. At low velocities, this arises from ideal flow of the superfluid. At higher velocities, the flow field is modified by excitations that are created when the flow velocity locally exceeds vL. The flow field causes Andreev reflection of quasiparticles and thus leads to change in the drag force. We calculate multiple limiting cases for a cylinder-shaped object. In the absence of quasiparticle-quasiparticle collisions, we find that the critical velocity is larger than vL and the drag force (per cross-sectional area) at 2vL is reduced by an order of magnitude compared to the case of a small object. In a collision-dominated limit, the flow shows signs of instability at a velocity belowvL

Engineering Filamentous Fungi for Conversion of d

d-Galacturonic acid, the main monomer of pectin, is an attractive substrate for bioconversions, since pectin-rich biomass is abundantly available and pectin is easily hydrolyzed. l-Galactonic acid is an intermediate in the eukaryotic pathway for d-galacturonic acid catabolism, but extracellular accumulation of l-galactonic acid has not been reported. By deleting the gene encoding l-galactonic acid dehydratase (lgd1 or gaaB) in two filamentous fungi, strains were obtained that converted d-galacturonic acid to l-galactonic acid. Both Trichoderma reesei Δlgd1 and Aspergillus niger ΔgaaB strains produced l-galactonate at yields of 0.6 to 0.9 g per g of substrate consumed. Although T. reesei Δlgd1 could produce l-galactonate at pH 5.5, a lower pH was necessary for A. niger ΔgaaB. Provision of a cosubstrate improved the production rate and titer in both strains. Intracellular accumulation of l-galactonate (40 to 70 mg g biomass(−1)) suggested that export may be limiting. Deletion of the l-galactonate dehydratase from A. niger was found to delay induction of d-galacturonate reductase and overexpression of the reductase improved initial production rates. Deletion of the l-galactonate dehydratase from A. niger also delayed or prevented induction of the putative d-galacturonate transporter An14g04280. In addition, A. niger ΔgaaB produced l-galactonate from polygalacturonate as efficiently as from the monomer

A novel pathway for fungal D-glucuronate catabolism contains an L-idonate forming 2-keto-L-gulonate reductase

For the catabolism of D-glucuronate, different pathways are used by different life forms. The pathways in bacteria and animals are established, however, a fungal pathway has not been described. In this communication, we describe an enzyme that is essential for D-glucuronate catabolism in the filamentous fungus Aspergillus niger. The enzyme has an NADH dependent 2-keto-L-gulonate reductase activity forming L-idonate. The deletion of the corresponding gene, the gluC, results in a phenotype of no growth on D-glucuronate. The open reading frame of the A. niger 2-keto-L-gulonate reductase was expressed as an active protein in the yeast Saccharomyces cerevisiae. A histidine tagged protein was purified and it was demonstrated that the enzyme converts 2-keto-L-gulonate to L-idonate and, in the reverse direction, L-idonate to 2-keto-L-gulonate using the NAD(H) as cofactors. Such an L-idonate forming 2-keto-L-gulonate dehydrogenase has not been described previously. In addition, the finding indicates that the catabolic D-glucuronate pathway in A. niger differs fundamentally from the other known D-glucuronate pathways