The tetrameric E. coli single stranded (ss)DNA binding protein (Ec-SSB) functions in DNA metabolism by binding to single stranded (ss) DNA and interacting directly with numerous DNA repair and replication proteins. Ec-SSB tetramers can bind ssDNA in multiple DNA binding modes that differ in the extent of ssDNA wrapping. Here, we show that the structurally similar SSB protein from the malarial parasite Plasmodium falciparum (Pf-SSB) also binds tightly to ssDNA, but does not display the same number of ssDNA binding modes as Ec-SSB, binding ssDNA exclusively in fully wrapped complexes with site sizes of 52-65 nucleotides/tetramer. Pf-SSB does not transition to the more cooperative (SSB)35 DNA binding mode observed for Ec-SSB. Consistent with this, Pf-SSB tetramers also do not display the dramatic intra-tetramer negative cooperativity for binding of a second (dT)35 molecule that is evident in Ec-SSB. These findings highlight variations in the DNA binding properties of these two highly conserved homotetrameric SSB proteins and these differences might be tailored to suit their specific functions in the cell.

Some individuals remain HIV-seronegative despite repeated unprotected exposure to the virus. Recent observations led to a concept that acquired immunity plays a role in protection or at least in altered susceptibility to HIV-1 infection in highly exposed seronegative (ESN) individuals. Our aim was to study HIV-specific cellular immune response induced in parenterally and/or heterosexually ESN individuals. Nine seronegative injection drug users (IDUs), 10 seronegative individuals and 9 their HIV-positive sexual and/or IDU partners from the cohort of IDUs were included in the study. The discordant couples had unprotected sex, and some of seronegative partners also had parenteral exposure. Cell-mediated responses were measured in PBMCs by ex vivo IFN-γ-ELISpot and ICS combining IFN-γ, TNF-α and IL-2 after stimulation with four consensus peptide pools (Nef, Gag, RT, Env, subtype A-EE). Thirteen out of 19 (68%) seronegative study subjects had strong Nef peptide pool specific ELISpot responses, 3 (16%) subjects responded against Gag peptide pool, and 1 subject had RT peptide pool response. Nef peptide pool responses in ESN were as high as in seropositive subjects. The multiple HIV-specific cytokine production in both CD4+ and CD8+ T-cells was shown for several ESN subjects. The functional profiles of the immune responses were different between seronegative and HIV-positive study groups. Whether the observed cellular responses have any protective role against HIV needs to be further investigated.

The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical, and magnetic tweezers), in combination with ensemble methods, have been particularly useful for mechanistic studies of protein-nucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single-molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single-stranded DNA. These include single-stranded DNA binding proteins, recombinases (RecA/Rad51), and helicases/translocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the single-stranded DNA and the mechanistic and functional information that can result from detailed analysis of such movement. Expected final online publication date for the Annual Review of Biophysics Volume 41 is May 04, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Flow coefficients v_{n} for n=2, 3, 4, characterizing the anisotropic collective flow in Au+Au collisions at sqrt[s_{NN}]=200  GeV, are measured relative to event planes Ψ_{n}, determined at large rapidity. We report v_{n} as a function of transverse momentum and collision centrality, and study the correlations among the event planes of different order n. The v_{n} are well described by hydrodynamic models which employ a Glauber Monte Carlo initial state geometry with fluctuations, providing additional constraining power on the interplay between initial conditions and the effects of viscosity as the system evolves. This new constraint can serve to improve the precision of the extracted shear viscosity to entropy density ratio η/s.

Molecular epidemiological features of Mycobacterium tuberculosis strains among different patient groups in Russia have not been studied well. The aim of our study was to compare the genotypes of M. tuberculosis strains circulating among tuberculosis (TB) patients from different groups: homeless, human immunodeficiency virus (HIV)-infected, prisoners, and the general population of St. Petersburg citizens. One hundred and forty-two M. tuberculosis complex isolates from different TB patient groups were studied using the spacer oligonucleotide typing (spoligotyping) method. The majority of the studied M. tuberculosis isolates in all groups belonged to the Beijing family (55% among homeless; 77% among HIV-infected; 60% among the general population; 81% among prisoners). There were no significant differences in the Beijing family prevalence among homeless patients, HIV/TB co-infected patients, and the general population of TB patients. The lowest genetic diversity of the pathogen was detected among imprisoned patients. The results of our study demonstrate that M. tuberculosis strains circulating among patients from high-risk groups are also spread among the general population of St. Petersburg citizens.

We present measurements of J/ψ yields in d+Au collisions at sqrt[s(NN)]=200  GeV recorded by the PHENIX experiment and compare them with yields in p+p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/ψ rapidity (-2.2<y<2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.

Here, we investigate the role of sensory feedback in gait generation and transition by using a three-dimensional, neuro-musculo-mechanical model of a salamander with realistic physical parameters. Activation of limb and axial muscles were driven by neural output patterns obtained from a central pattern generator (CPG) which is composed of simulated spiking neurons with adaptation. The CPG consists of a body-CPG and four limb-CPGs that are interconnected via synapses both ipsilaterally and contralaterally. We use the model both with and without sensory modulation and four different combinations of ipsilateral and contralateral coupling between the limb-CPGs. We found that the proprioceptive sensory inputs are essential in obtaining a coordinated lateral sequence walking gait (walking). The sensory feedback includes the signals coming from the stretch receptor like intraspinal neurons located in the girdle regions and the limb stretch receptors residing in the hip and scapula regions of the salamander. On the other hand, walking trot gait (trotting) is more under central (CPG) influence compared to that of the peripheral or sensory feedback. We found that the gait transition from walking to trotting can be induced by increased activity of the descending drive coming from the mesencephalic locomotor region and is helped by the sensory inputs at the hip and scapula regions detecting the late stance phase. More neurophysiological experiments are required to identify the precise type of mechanoreceptors in the salamander and the neural mechanisms mediating the sensory modulation.

SSB proteins bind to and control the accessibility of single-stranded DNA (ssDNA), likely facilitated by their ability to diffuse on ssDNA. Using a hybrid single-molecule method combining fluorescence and force, we probed how proteins with large binding site sizes can migrate rapidly on DNA and how protein-protein interactions and tension may modulate the motion. We observed force-induced progressive unraveling of ssDNA from the SSB surface between 1 and 6 pN, followed by SSB dissociation at ∼10 pN, and obtained experimental evidence of a reptation mechanism for protein movement along DNA wherein a protein slides via DNA bulge formation and propagation. SSB diffusion persists even when bound with RecO and at forces under which the fully wrapped state is perturbed, suggesting that even in crowded cellular conditions SSB can act as a sliding platform to recruit and carry its interacting proteins for use in DNA replication, recombination and repair.

We have previously shown that formation of a 1:1 fully wrapped complex of Escherichia coli SSB tetramer with (dT)(70) displays a temperature-dependent sign reversal of the binding heat capacity (ΔC(P)). Here we examine SSB binding to shorter oligodeoxynucleotides ((dX)(35)) to probe whether this effect requires binding of one or two (dX)(35) molecules per SSB tetramer. We find that the ΔC(P) for the first molecule of (dX)(35) is always negative. However, a sign reversal of ΔC(P) from negative to positive occurs with increasing temperature for binding of the second (dX)(35). This striking behavior of ΔC(P) for the second (dX)(35) appears linked to conformational changes within the ssDNA-SSB complex that are required to form a fully wrapped (SSB)(65) binding mode. These results also underscore that binding heat capacities of macromolecular interactions have multiple origins that cannot be understood simply on the basis of examining static structures.

Plasma-assisted electron-beam evaporation leads to changes in the crystallinity, density, and stresses of thin films. A dual-source plasma system provides stress control of large-aperture, high-fluence coatings used in vacuum for substrates 1m in aperture.