\u3cem\u3ePlasmodium falciparum\u3c/em\u3e SSB Tetramer Wraps Single-Stranded DNA with Similar Topology but Opposite Polarity to \u3cem\u3eE. coli\u3c/em\u3e SSB

Single-stranded DNA binding (SSB) proteins play central roles in genome maintenance in all organisms. Plasmodium falciparum, the causative agent of malaria, encodes an SSB protein that localizes to the apicoplast and likely functions in the replication and maintenance of its genome. P. falciparum SSB (Pf-SSB) shares a high degree of sequence homology with bacterial SSB proteins but differs in the composition of its C-terminus, which interacts with more than a dozen other proteins in Escherichia coli SSB (Ec-SSB). Using sedimentation methods, we show that Pf-SSB forms a stable homo-tetramer alone and when bound to single-stranded DNA (ssDNA). We also present a crystal structure at 2.1 Å resolution of the Pf-SSB tetramer bound to two (dT)35 molecules. The Pf-SSB tetramer is structurally similar to the Ec-SSB tetramer, and ssDNA wraps completely around the tetramer with a “baseball seam” topology that is similar to Ec-SSB in its “65 binding mode”. However, the polarity of the ssDNA wrapping around Pf-SSB is opposite to that observed for Ec-SSB. The interactions between the bases in the DNA and the amino acid side chains also differ from those observed in the Ec-SSB–DNA structure, suggesting that other differences may exist in the DNA binding properties of these structurally similar proteins

Spatial and temporal cellular responses to single-strand breaks in human cells

DNA single-strand breaks (SSB) are one of the most frequent DNA lesions produced by reactive oxygen species and during DNA metabolism, but the analysis of cellular responses to SSB remains difficult due to the lack of an experimental method to produce SSB alone in cells. By using human cells expressing a foreign UV damage endonuclease (UVDE) and irradiating the cells with UV through tiny pores in membrane filters, we created SSB in restricted areas in the nucleus by the immediate action of UVDE on UV-induced DNA lesions. Cellular responses to the SSB were characterized by using antibodies and fluorescence microscopy. Upon UV irradiation, poly(ADP-ribose) synthesis occurred immediately in the irradiated area. Simultaneously, but dependent on poly(ADP-ribosyl)ation, XRCC1 was translocated from throughout the nucleus, including nucleoli, to the SSB. The BRCT1 domain of XRCC1 protein was indispensable for its poly(ADP-ribose)-dependent recruitment to the SSB. Proliferating cell nuclear antigen and the p150 subunit of chromatin assembly factor 1 also accumulated at the SSB in a detergent-resistant form, which was significantly reduced by inhibition of poly(ADP-ribose) synthesis. Our results show the importance of poly(ADP-ribosyl)ation in sequential cellular responses to SSB

Multiple C-Terminal Tails within a Single \u3cem\u3eE. coli\u3c/em\u3e SSB Homotetramer Coordinate DNA Replication and Repair

Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold “tetramer”. Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance

SSB-1 of the yeast Saccharomyces cerevisiae is a nucleolar-specific, silver-binding protein that is associated with the snR10 and snR11 small nuclear RNAs

SSB-1, the yeast single-strand RNA-binding protein, is demonstrated to be a yeast nucleolar-specific, silver-binding protein. In double-label immunofluorescence microscopy experiments antibodies to two other nucleolar proteins, RNA Pol I 190-kD and fibrillarin, were used to reveal the site of rRNA transcription; i.e., the fibrillar region of the nucleolus. SSB-1 colocalized with fibrillarin in a double-label immunofluorescence mapping experiment to the yeast nucleolus. SSB-1 is located, though, over a wider region of the nucleolus than the transcription site marker. Immunoprecipitations of yeast cell extracts with the SSB-1 antibody reveal that in 150 mM NaCl SSB-1 is bound to two small nuclear RNAs (snRNAs). These yeast snRNAs are snR10 and snR11, with snR10 being predominant. Since snR10 has been implicated in pre-rRNA processing, the association of SSB-1 and snR10 into a nucleolar snRNP particle indicates SSB-1 involvement in rRNA processing as well. Also, another yeast protein, SSB-36-kD, isolated by single- strand DNA chromatography, is shown to bind silver under the conditions used for nucleolar-specific staining. It is, most likely, another yeast nucleolar protein

Symmetry breaking, Josephson oscillation and self-trapping in a self-bound three-dimensional quantum ball

We study spontaneous symmetry breaking (SSB), Josephson oscillation, and self-trapping in a stable, mobile, three-dimensional matter-wave spherical quantum ball self-bound by attractive two-body and repulsive three-body interactions. The SSB is realized by a parity-symmetric (a) one-dimensional (1D) double-well potential and (b) a 1D Gaussian potential, both along the $z$ axis and no potential along the $x$ and $y$ axes. In the presence of each of these potentials, the symmetric ground state dynamically evolves into a doubly-degenerate SSB ground state. If the SSB ground state in the double well, predominantly located in the first well ($z>0$), is given a small displacement, the quantum ball oscillates with a self-trapping in the first well. For a medium displacement one encounters an asymmetric Josephson oscillation. The asymmetric oscillation is a consequence of SSB. The study is performed by a variational and numerical solution of a non-linear mean-field model with 1D parity-symmetric perturbations

The Effects of the Quantification of Faculty Productivity: Perspectives from the Design Science Research Community

In recent years, efforts to assess faculty research productivity have focused more on the measurable quantification of academic outcomes. For benchmarking academic performance, researchers have developed different ranking and rating lists that define so-called high-quality research. While many scholars in IS consider lists such as the Senior Scholar’s basket (SSB) to provide good guidance, others who belong to less-mainstream groups in the IS discipline could perceive these lists as constraining. Thus, we analyzed the perceived impact of the SSB on information systems (IS) academics working in design science research (DSR) and, in particular, how it has affected their research behavior. We found the DSR community felt a strong normative influence from the SSB. We conducted a content analysis of the SSB and found evidence that some of its journals have come to accept DSR more. We note the emergence of papers in the SSB that outline the role of theory in DSR and describe DSR methodologies, which indicates that the DSR community has rallied to describe what to expect from a DSR manuscript to the broader IS community and to guide the DSR community on how to organize papers for publication in the SSB

\u3cem\u3ePlasmodium falciparum\u3c/em\u3e SSB Tetramer Binds Single-Stranded DNA Only in a Fully Wrapped Mode

The tetrameric Escherichia coli single-stranded DNA (ssDNA) binding protein (Ec-SSB) functions in DNA metabolism by binding to ssDNA 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 nt/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

Threshold corrections to the radiative breaking of electroweak symmetry and neutralino dark matter in supersymmetric seesaw model

We study the radiative electroweak symmetry breaking and the relic abundance of neutralino dark matter in the supersymmetric type I seesaw model. In this model, there exist threshold corrections to Higgs bilinear terms coming from heavy singlet sneutrino loops, which make the soft supersymmetry breaking (SSB) mass for up-type Higgs shift at the seesaw scale and thus a minimization condition for the Higgs potential is affected. We show that the required fine-tuning between the Higgsino mass parameter mu and the SSB mass for up-type Higgs may be reduced at the electroweak scale, due to the threshold corrections. We also present how the parameter mu depends on the SSB B-parameter for heavy singlet sneutrinos. Since the property of neutralino dark matter is quite sensitive to the size of mu, we discuss how the relic abundance of neutralino dark matter is affected by the SSB B-parameter. Taking the SSB B-parameter of order of a few hundreds TeV, the required relic abundance of neutralino dark matter can be correctly achieved. In this case, dark matter is a mixture of bino and Higgsino, under the condition that gaugino masses are universal at the grand unification scale.Comment: 27 pages, 3 figures; references added, discussion about RGEs added, the version published on PR

Perturbative Unification of Soft Supersymmetry--Breaking Terms

Perturbative unification of soft supersymmetry--breaking (SSB) parameters is proposed in Gauge-Yukawa unified models. The method, which can be applied in any finite order in perturbation theory, consists in searching for renormalization group invariant relations among the SSB parameters, which are consistent with perturbative renormalizability. For the minimal Gauge-Yukawa unified model based on $SU(5)$ we find that the low energy SSB sector contains a single arbitrary parameter, the unified gaugino mass. Within a certain approximation we find that the model predicts a superpartner spectrum which is consistent with the experimental data.Comment: 14 page