Lateral diffusion on tubular membranes: quantification of measurements bias

Single Particle Tracking (SPT) is a powerful technique for the analysis of the lateral diffusion of the lipid and protein components of biological membranes. In neurons, SPT allows the study of the real-time dynamics of receptors for neurotransmitters that diffuse continuously in and out synapses. In the simplest case where the membrane is flat and is parallel to the focal plane of the microscope the analysis of diffusion from SPT data is relatively straightforward. However, in most biological samples the membranes are curved, which complicates analysis and may lead to erroneous conclusions as for the mode of lateral diffusion. Here we considered the case of lateral diffusion in tubular membranes, such as axons, dendrites or the neck of dendritic spines. Monte Carlo simulations allowed us to evaluate the error in diffusion coefficient (D) calculation if the curvature is not taken into account. The underestimation is determined by the diameter of the tubular surface, the frequency of image acquisition and the degree of mobility itself. We found that projected trajectories give estimates that are 25 to 50% lower than the real D in case of 2D-SPT over the tubular surface. The use of 3D-SPT improved the measurements if the frequency of image acquisition was fast enough in relation to the mobility of the molecules and the diameter of the tube. Nevertheless, the calculation of D from the components of displacements in the axis of the tubular structure gave accurate estimate of D, free of geometrical artefacts. We show the application of this approach to analyze the diffusion of a lipid on model tubular membranes and of a membrane-bound GFP on neurites from cultured rat hippocampal neurons.     

High Resolution Genome-Wide Analysis of Chromosomal Alterations in Burkitt's Lymphoma

Additional chromosomal abnormalities are currently detected in Burkitt''s lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt''s lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs<2 Mb were mapped to Mendelian CNVs, including GSTT1, glutathione s-transferase and BIRC6, an anti-apoptotic protein, possibly predisposing to some cancers. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs >2 Mb, gains were found in 1q (12/27), 13q (7/27), 7q (6/27), 8q(4/27), 2p (3/27), 11q (2/27) and 15q (2/27). Losses were found in 3p (5/27), 4p (4/27), 4q (4/27), 9p (4/27), 13q (4/27), 6p (3/27), 17p (3/27), 6q (2/27),11pterp13 (2/27) and 14q12q21.3 (2/27). Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32.1 <89.58–96.81> MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 <60.96–61> MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 <60.43–60.53> that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies.     

3D genomics imposes evolution of the domain model of eukaryotic genome organization

The hypothesis that the genome is composed of a patchwork of structural and functional domains (units) that may be either active or repressed was proposed almost 30 years ago. Here, we examine the evolution of the domain model of eukaryotic genome organization in view of the expansion of genome-scale techniques in the twenty-first century that have provided us with a wealth of information on genome organization, folding, and functioning.     

Cytochrome c location in phosphatidylcholine/cardiolipin model membranes: resonance energy transfer study

Resonance energy transfer between lipid-bound fluorescent probe 3-methoxybenzanthrone as a donor and heme group of cytochrome c as an acceptor has been examined to ascertain the protein disposition relative to the surface of model membranes composed of phosphatidylcholine and cardiolipin (10, 50 and 80 mol%). The model of energy transfer in membrane systems has been extended to the case of donors distributed between the two-bilayer leaflets and acceptors located at the outer monolayer taking into account the donor and acceptor orientational behavior. Assuming specific protein orientation relative to the membrane surface and varying lateral distance of the donor-acceptor closest approach in the range from 0 to 3.5 nm the limits for possible heme distances from the bilayer midplane have been found to be 0.8-3 nm (10 mol% CL), 0-2.6 nm (50 mol% CL), and 1.4-3.3 nm (80 mol% CL).     

From an increase in the number of tandem repeats through the decrease of sialylation to the downregulation of MUC1 expression level

Enhanced glucose uptake by cancer cells was demonstrated in many studies in vitro and in vivo. Glycolysis is one of the main ways of obtaining energy in hypoxia conditions. However, in addition to energy exchange, carbohydrates are also necessary for the posttranslational modification of the protein molecules. Cancer cells are often characterized by an enhanced expression of different glycoproteides. Correct glycosylation defines the structure and activity of such molecules. We demonstrated that under the same cultivation conditions, the intensity of glycosylation does not depend on the total number of potential O-glycosylation sites in one molecule. As a model for the investigation, the tandem repeat region (region with variable number of tandem repeats) of the human mucin MUC1, in which each of the repeats carries four potential O-glycosylation sites, was used. An increase of the tandem repeat number in the recombinant protein did not lead to a proportional increase in the level of sLe^a glycosides. A consequence of this was a reduction in the number of recombinant proteins associated with the cytoplasmic membrane at an overall high expression level. Prolongation of the cultivation duration led to a reduction in the expression level of the recombinant proteins by up to 30% of the initial level, and the intensity of this reduction was in a direct ratio to the number of tandem repeats in the protein molecule.     

NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions

In order to examine the origins of the large positive cooperativity (ΔG(0)(coop) = -2.9 kcal mol(-1)) of trimethoprim (TMP) binding to a bacterial dihydrofolate reductase (DHFR) in the presence of NADPH, we have determined and compared NMR solution structures of L. casei apo DHFR and its binary and ternary complexes with TMP and NADPH and made complementary thermodynamic measurements. The DHFR structures are generally very similar except for the A-B loop region and part of helix B (residues 15-31) which could not be directly detected for L. casei apo DHFR because of line broadening from exchange between folded and unfolded forms. Thermodynamic and NMR measurements suggested that a significant contribution to the cooperativity comes from refolding of apo DHFR on binding the first ligand (up to -0.95 kcals mol(-1) if 80% of A-B loop requires refolding). Comparisons of Cα-Cα distance differences and domain rotation angles between apo DHFR and its complexes indicated that generally similar conformational changes involving domain movements accompany formation of the binary complexes with either TMP or NADPH and that the binary structures are approaching that of the ternary complex as would be expected for positive cooperativity. These favorable ligand-induced structural changes upon binding the first ligand will also contribute significantly to the cooperative binding. A further substantial contribution to cooperative binding results from the proximity of the bound ligands in the ternary complex: this reduces the solvent accessible area of the ligand and provides a favorable entropic hydrophobic contribution (up to -1.4 kcal mol(-1)).     

Visual laterality of calf-mother interactions in wild whales

Background

Behavioral laterality is known for a variety of vertebrate and invertebrate animals. Laterality in social interactions has been described for a wide range of species including humans. Although evidence and theoretical predictions indicate that in social species the degree of population level laterality is greater than in solitary ones, the origin of these unilateral biases is not fully understood. It is especially poorly studied in the wild animals. Little is known about the role, which laterality in social interactions plays in natural populations. A number of brain characteristics make cetaceans most suitable for investigation of lateralization in social contacts.

Methodology/Principal Findings

Observations were made on wild beluga whales (Delphinapterus leucas) in the greatest breeding aggregation in the White Sea. Here we show that young calves (in 29 individually identified and in over a hundred of individually not recognized mother-calf pairs) swim and rest significantly longer on a mother''s right side. Further observations along with the data from other cetaceans indicate that found laterality is a result of the calves'' preference to observe their mothers with the left eye, i.e., to analyze the information on a socially significant object in the right brain hemisphere.

Conclusions/Significance

Data from our and previous work on cetacean laterality suggest that basic brain lateralizations are expressed in the same way in cetaceans and other vertebrates. While the information on social partners and novel objects is analyzed in the right brain hemisphere, the control of feeding behavior is performed by the left brain hemisphere. Continuous unilateral visual contacts of calves to mothers with the left eye may influence social development of the young by activation of the contralateral (right) brain hemisphere, indicating a possible mechanism on how behavioral lateralization may influence species life and welfare. This hypothesis is supported by evidence from other vertebrates.