Studies of cis- and trans-acting elements in Tetrahymena rDNA replication

Eukaryotic cells must precisely duplicate their genomes before they divide. The mechanisms of eukaryotic chromosomal DNA replication are far from clear, however, because very few cis- and trans-acting factors that function in eukaryotic DNA replication have been identified. To gain further insights into this problem, this work identified and characterized potential cis- and trans-acting replication factors for the replication initiation of Tetrahymena ribosomal RNA gene (rDNA);A search far cis-acting elements identified a cluster of predicted modular sequences and structural elements in the origin region of rDNA. The presence of these elements were verified experimentally; (1) two mung bean nuclease-hypersensitive sites were localized within the 5\u27NTS; (2) three fragments in the 5\u27NTS were found to contain bent DNA structures; (3) nuclear matrices were found to be present in the 5\u27NTS. These structural elements were also identified in five other eukaryotic origin regions, suggesting that clusters of modular structural elements may be a conserved feature in eukaryotic chromosomal origins of replication;Biochemical purification of potential trans-acting factors has led to the identification of the first DNA helicase in protozoan, Tetrahymena thermophila DNA helicase I. It co-fractionated through several steps with ssA-TIBF, an rDNA origin binding protein, indicating that they may functionally associate in rDNA replication in vivo. The ATP-binding subunit was determined to be ~70 kDa, distinct from the 24 kDa DNA binding subunit of ssA-TIBF. The directionality of this helicase was 3\u27 to 5\u27, indicating a possible functional interaction with DNA polymerase moving in the same direction during DNA replication. This helicase preferentially unwound helicase substrates containing a fork-like structure which resembles replication intermediates. Taken together, the properties of T. thermophila DNA helicase I suggest that it could function as a replicative helicase in leading strand DNA synthesis. A model is proposed to describe possible events in the replication initiation of Tetrahymena rDNA

BRST-antifield-treatment of metric-affine gravity

The metric-affine gauge theory of gravity provides a broad framework in which gauge theories of gravity can be formulated. In this article we fit metric-affine gravity into the covariant BRST--antifield formalism in order to obtain gauge fixed quantum actions. As an example the gauge fixing of a general two-dimensional model of metric-affine gravity is worked out explicitly. The result is shown to contain the gauge fixed action of the bosonic string in conformal gauge as a special case.Comment: 19 pages LATEX, to appear in Phys. Rev.

MicroRNA-196a-5p targeting LRP1B modulates phenotype of thyroid carcinoma cells

Introduction: Thyroid cancer (TC) is a common endocrine malignancy, comprising nearly one-third of all head and neck malignancies worldwide. MicroRNAs (miRNAs) have been implicated in the malignant progression of multiple cancers; however, their contribution to thyroid diseases has not been fully explored. Material and methods: This study aimed to illustrate the regulatory mechanism of microRNA-196a-5p in TC progression and to investigate whether microRNA-196a-5p affects progression of TC cells by targeting low-density lipoprotein receptor-associated protein 1B (LRP1B). MicroRNA-196a-5p and LRP1B expression status in TC cells and normal human thyroid cells was detected by quantative reverse transcription polymerase chain reaction (qRT-PCR) and western blot. Dual-luciferase reporter assay, cell counting kit-8 (CCK-8) assay, scratch healing assay, and Transwell assay were also performed. Results: The results showed that microRNA-196a-5p expression was up-regulated and LRP1B expression was down regulated in TC cells. In addition, the upregulation of microRNA-196a-5p facilitated progression of TC cells. Silencing microRNA-196a-5p led to the opposite results. Dual-luciferase reporter assay offered evidence for microRNA-196a-5p targeting LRP1B in TC. MicroRNA-196a-5p could target LRP1B to facilitate proliferation, invasion, and migration of TC cells. Conclusion: Overall, this study revealed that microRNA-196a-5p may be a cancer-promoting microRNA that plays an important role in TC progression

No genetic link between Parkinson’s disease and SARS-CoV-2 infection: a two-sample Mendelian randomization study

ObjectiveExisting literature has not clearly elucidated whether SARS-CoV-2 infection increases the incidence of Parkinson’s disease or if Parkinson’s disease patients are more susceptible to the effects of SARS-CoV-2 infection. To clarify the issue, this study employs a genetic epidemiological approach to investigate the association.MethodsThis study utilizes a two-sample Mendelian randomization analysis. The primary analysis employs the inverse variance-weighted (IVW) method, supplemented by secondary analyses including MR-Egger regression, weighted median, IVW radial method, and weighted mode, to evaluate the bidirectional causal relationship between Parkinson’s disease and SARS-CoV-2 infection.ResultsIVW results showed no genetic causality between SARS-CoV-2 susceptibility, hospitalization rate and severity and Parkinson’s disease. (IVW method: p = 0.408 OR = 1.10 95% CI: 0.87 ~ 1.39; p = 0.744 OR = 1.11 95% CI: 0.94 ~ 1.09; p = 0.436 OR = 1.05 95% CI: 0.93 ~ 1.17). Parkinson’s disease was not genetically associated with susceptibility to new crown infections, hospitalization rates, and severity (IVW method: p = 0.173 OR = 1.01 95% CI: 0.99 ~ 1.03; p = 0.109 OR = 1.05 95% CI: 0.99 ~ 1.12; p = 0.209 OR = 1.03 95% CI: 0.99 ~ 1.07). MR-Egger regression, weighted median, IVW radial method, and weighted mode results are consistent with the results of the IVW method.ConclusionThis study does not support a genetic link between Parkinson’s disease and SARS-CoV-2 infection, and the association observed in previous cohort studies and observational studies may be due to other confounding factors

RETRACTED: DNA-PKcs-PIDDosome: A Nuclear Caspase-2-Activating Complex with Role in G2/M Checkpoint Maintenance

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the Authors.Our paper reported the identification of a nuclear protein complex comprising DNA-PKcs, PIDD, and caspase-2 and characterization of its role in G2/M checkpoint maintenance, thereby providing insight into the functional significance of nuclear caspase-2. We recently identified errors affecting several figure panels where original data were processed inappropriately such that the figure panels do not accurately report the original data. We believe that the most responsible course of action is to retract the paper. We sincerely apologize to the scientific community for any inconvenience this might cause

Diverse Applications of Nanomedicine

The design and use of materials in the nanoscale size range for addressing medical and health-related issues continues to receive increasing interest. Research in nanomedicine spans a multitude of areas, including drug delivery, vaccine development, antibacterial, diagnosis and imaging tools, wearable devices, implants, high-throughput screening platforms, etc. using biological, nonbiological, biomimetic, or hybrid materials. Many of these developments are starting to be translated into viable clinical products. Here, we provide an overview of recent developments in nanomedicine and highlight the current challenges and upcoming opportunities for the field and translation to the clinic. \ua9 2017 American Chemical Society

On the issue of transparency and reproducibility in nanomedicine.

Following our call to join in the discussion over the suitability of implementing a reporting checklist for bio-nano papers, the community responds

Studies of cis- and trans-acting elements in Tetrahymena rDNA replication

Eukaryotic cells must precisely duplicate their genomes before they divide. The mechanisms of eukaryotic chromosomal DNA replication are far from clear, however, because very few cis- and trans-acting factors that function in eukaryotic DNA replication have been identified. To gain further insights into this problem, this work identified and characterized potential cis- and trans-acting replication factors for the replication initiation of Tetrahymena ribosomal RNA gene (rDNA);A search far cis-acting elements identified a cluster of predicted modular sequences and structural elements in the origin region of rDNA. The presence of these elements were verified experimentally; (1) two mung bean nuclease-hypersensitive sites were localized within the 5'NTS; (2) three fragments in the 5'NTS were found to contain bent DNA structures; (3) nuclear matrices were found to be present in the 5'NTS. These structural elements were also identified in five other eukaryotic origin regions, suggesting that clusters of modular structural elements may be a conserved feature in eukaryotic chromosomal origins of replication;Biochemical purification of potential trans-acting factors has led to the identification of the first DNA helicase in protozoan, Tetrahymena thermophila DNA helicase I. It co-fractionated through several steps with ssA-TIBF, an rDNA origin binding protein, indicating that they may functionally associate in rDNA replication in vivo. The ATP-binding subunit was determined to be ~70 kDa, distinct from the 24 kDa DNA binding subunit of ssA-TIBF. The directionality of this helicase was 3' to 5', indicating a possible functional interaction with DNA polymerase moving in the same direction during DNA replication. This helicase preferentially unwound helicase substrates containing a fork-like structure which resembles replication intermediates. Taken together, the properties of T. thermophila DNA helicase I suggest that it could function as a replicative helicase in leading strand DNA synthesis. A model is proposed to describe possible events in the replication initiation of Tetrahymena rDNA.</p

The UBC Domain Is Required for BRUCE to Promote BRIT1/MCPH1 Function in DSB Signaling and Repair Post Formation of BRUCE-USP8-BRIT1 Complex.

BRUCE is implicated in the regulation of DNA double-strand break response to preserve genome stability. It acts as a scaffold to tether USP8 and BRIT1, together they form a nuclear BRUCE-USP8-BRIT1 complex, where BRUCE holds K63-ubiquitinated BRIT1 from access to DSB in unstressed cells. Following DSB induction, BRUCE promotes USP8 mediated deubiquitination of BRIT1, a prerequisite for BRIT1 to be released from the complex and recruited to DSB by binding to γ-H2AX. BRUCE contains UBC and BIR domains, but neither is required for the scaffolding function of BRUCE mentioned above. Therefore, it remains to be determined whether they are required for BRUCE in DSB response. Here we show that the UBC domain, not the BIR domain, is required for BRUCE to promote DNA repair at a step post the formation of BRUCE-USP8-BRIT1 complex. Mutation or deletion of the BRUCE UBC domain did not disrupt the BRUCE-USP8-BRIT1 complex, but impaired deubiquitination and consequent recruitment of BRIT1 to DSB. This leads to impaired chromatin relaxation, decreased accumulation of MDC1, NBS1, pATM and RAD51 at DSB, and compromised homologous recombination repair of DNA DSB. These results demonstrate that in addition to the scaffolding function in complex formation, BRUCE has an E3 ligase function to promote BRIT1 deubiquitination by USP8 leading to accumulation of BRIT1 at DNA double-strand break. These data support a crucial role for BRUCE UBC activity in the early stage of DSB response

Generation and Analysis of Attack Graphs

AbstractAn integral part of modeling the global view of network security is constructing attack graphs. Construction by hand, however, is tedious, error prone, and impractical for attack graphs larger than a hundred nodes. In this paper we present an automated technique for generating and analyzing attack graphs. We base our technique on symbolic model checking algorithms, letting us construct attack graphs automatically and efficiently. We also describe two analyses to help decide which attacks would be most costeffective to guard against. We implemented our technique in a tool suite and tested it on a small network example, which includes models of a firewall and an intrusion detection system