Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo‐tomography

We employed electron cryo‐tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation‐arrested ribosomes reveal the clustered organization of the TOM complex, corroborating earlier reports of localized translation. Ribosomes are shown to interact specifically with the TOM complex, and nascent chain binding is crucial for ribosome recruitment and stabilization. Ribosomes are bound to the membrane in discrete clusters, often in the vicinity of the crista junctions. This interaction highlights how protein synthesis may be coupled with transport. Our work provides unique insights into the spatial organization of cytosolic ribosomes on mitochondria.     

The complexity of selection at the major primate β-defensin locus

Background  

We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mouse. For the first time these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as the ancient past. We have used a combination of maximum likelihood based tests and a maximum parsimony based sliding window approach to give a detailed view of the varying modes of selection operating at this locus.     

Previtamin D3 with a trans-fused decalin CD-ring has pronounced genomic activity

Deletion of C19 in the structure of 1 alpha,25-dihydroxyvitamin D3 [1,25(OH)2D3] does not substantially alter the biological potency but prevents the conversion between the vitamin and the previtamin form. Hence, this modification allows the study of locked previtamin and vitamin forms. The locked 19-nor-1,25(OH)2-previtamin D3 analog (19-nor-previtamin D) had a low biological activity and was a rather weak activator of the genomic signal transduction pathway. 19-Nor-trans-decalin-1,25(OH)2-vitamin D3 (19-nor-TD-vitamin D), characterized by the presence of a trans-fused decalin CD-ring system, was 10-fold more potent than the parent compound and was a potent activator of the genomic signal transduction pathway. Surprisingly, the previtamin, 19-nor-trans-decalin-1,25(OH)2-previtamin D3 (19-nor-TD-previtamin D), was as potent as 1,25(OH)2D3 in inhibiting cell proliferation and inducing cell differentiation and represents the first previtamin structure with pronounced vitamin D-like activity. Furthermore, this compound interacted as efficiently as 1,25(OH)2D3 with the vitamin D receptor (VDR), retinoid X receptor (RXR), coactivators, and DNA, which illustrated its potent ability to activate the genomic signal transduction pathway. Analysis of the transactivation potency of 12 VDR point mutants after stimulation with 19-nor-TD-previtamin D revealed that this analog used the same contact points within the receptor as did 1,25(OH)2D3. This could be confirmed by modeling analysis of this compound in the ligand binding pocket of VDR. In conclusion, a previtamin D3 analog is presented with genomic activities equivalent to 1,25(OH)2D3.     

Protein tyrosine nitration in the mitochondria from diabetic mouse heart. Implications to dysfunctional mitochondria in diabetes

Oxidative stress has been implicated in dysfunctional mitochondria in diabetes. Tyrosine nitration of mitochondrial proteins was observed under conditions of oxidative stress. We hypothesize that nitration of mitochondrial proteins is a common mechanism by which oxidative stress causes dysfunctional mitochondria. The putative mechanism of nitration in a diabetic model of oxidative stress and functional changes of nitrated proteins were studied in this work. As a source of mitochondria, alloxan-susceptible and alloxan-resistant mice were used. These inbred strains are distinguished by the differential ability to detoxify free radicals. A proteomic approach revealed significant similarity between patterns of tyrosine-nitrated proteins generated in the heart mitochondria under different in vitro and in vivo conditions of oxidative stress. This observation points to a common nitrating species, which may derive from different nitrating pathways in vivo and may be responsible for the majority of nitrotyrosine formed. Functional studies show that protein nitration has an adverse effect on protein function and that protection against nitration protects functional properties of proteins. Because proteins that undergo nitration are involved in major mitochondrial functions, such as energy production, antioxidant defense, and apoptosis, we concluded that tyrosine nitration of mitochondrial proteins may lead to dysfunctional mitochondria in diabetes.     

Evolution of energy metabolism and its compartmentation in Kinetoplastida

Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties.     

Macroscale modeling of cartilage: mixture theory versus homogenization

The equations governing the electro-chemo-hydro-mechanical processes in cartilage are derived using the periodic homogenization technique. First the equations at the microscale are recalled. Then the homogenization technique is applied to propagate the physics to the macroscale. The results of this work and of the thermodynamical approach used by various authors are finally compared.     

POSA: Perl Objects for DNA Sequencing Data Analysis

Background  

Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines.     

Mechanisms of the gravitational sensitivity of cells

It is well known that specialized gravireceptory cells have been formed in the course of evolution in the majority of multicellular organisms. These are statosytes (statenchyme cells) in higher plants and otolith apparatus cells in animals. The mechanisms of gravity reception and the generation of gravitational stimuli in these cells are well understood. Therefore, our attention was focused on cells devoid of special gravireceptory mechanisms, namely cell cultures grown in vitro (fibroblasts and osteoblasts) and unicellular free-swimming (i.e. possessing a locomotor apparatus) organisms. These were mainly representatives of two classes: Ciliata and Flagellata. The choice of the objects of study was mainly determined by their ecological and physiological characteristics with the main goals of this work.     

Biochemical basis for depressed serum retinol levels in transthyretin-deficient mice

Transthyretin (TTR) acts physiologically in the transport of retinol in the circulation. We previously reported the generation and partial characterization of TTR-deficient (TTR(-)) mice. TTR(-) mice have very low circulating levels of retinol and its specific transport protein, retinol-binding protein (RBP). We have examined the biochemical basis for the low plasma retinol-RBP levels. Cultured primary hepatocytes isolated from wild type (WT) and TTR(-) mice accumulated RBP in their media to an identical degree, suggesting that RBP was being secreted from the hepatocytes at the same rate. In vivo experiments support this conclusion. For the first 11 h after complete nephrectomy, the levels retinol and RBP rose in the circulations of WT and TTR(-) mice at nearly identical rates. However, human retinol-RBP injected intravenously was more rapidly cleared from the circulation (t(12) = 0.5 h for TTR(-) versus t(12) >6 h for WT) and accumulated faster in the kidneys of TTR(-) compared with WT mice. The rate of infiltration of the retinol-RBP complex from the circulation to tissue interstitial fluids was identical in both strains. Taken together, these data indicate that low circulating retinol-RBP levels in TTR(-) mice arise from increased renal filtration of the retinol-RBP complex.     

Heart rate modulates the slow enhancement of contraction due to sudden left ventricular dilation

In isovolumic blood-perfused dog hearts, left ventricular developed pressure (DP) was recorded while a sudden ventricular dilation was promoted at three heart rate (HR) levels: low (L: 52 +/- 1.7 beats/min), intermediate (M: 82 +/- 2.2 beats/min), and high (H: 117 +/- 3.5 beats/min). DP increased instantaneously with chamber expansion (Delta(1)DP), and another continuous increase occurred for several minutes (Delta(2)DP). HR elevation did not alter Delta(1)DP (32.8 +/- 1.6, 33.6 +/- 1.5, and 34.3 +/- 1.2 mmHg for L, M, and H, respectively), even though it intensified Delta(2)DP (17.3 +/- 0.9, 20.7 +/- 1.0, and 26.8 +/- 1.2 mmHg for L, M, and H, respectively), meaning that the treppe phenomenon enhances the length dependence of the contraction component related to changes in intracellular Ca(2+) concentration. Frequency increments reduced the half time of the slow response (82 +/- 3.6, 67 +/- 2.6, and 53 +/- 2.0 s for L, M, and H, respectively), while the number of beats included in half time increased (72 +/- 2.9, 95 +/- 2.9, and 111 +/- 3.2 beats for L, M, and H, respectively). HR modulation of the slow response suggests that L-type Ca(2+) channel currents and/or the Na(+)/Ca(2+) exchanger plays a relevant role in the stretch-triggered Ca(2+) gain when HR increases in the canine heart.