Directional mechanical stability of Bacteriophage φ29 motor’s 3WJ-pRNA: Extraordinary robustness along portal axis

The molecular motor exploited by bacteriophage φ29 to pack DNA into its capsid is regarded as one of the most powerful mechanical devices present in viral, bacterial, and eukaryotic systems alike. Acting as a linker element, a prohead RNA (pRNA) effectively joins the connector and ATPase (adenosine triphosphatase) components of the φ29 motor. During DNA packing, this pRNA needs to withstand enormous strain along the capsid’s portal axis—how this remarkable stability is achieved remains to be elucidated. We investigate the mechanical properties of the φ29 motor’s three-way junction (3WJ)–pRNA using a combined steered molecular dynamics and atomic force spectroscopy approach. The 3WJ exhibits strong resistance to stretching along its coaxial helices, demonstrating its super structural robustness. This resistance disappears, however, when external forces are applied to the transverse directions. From a molecular standpoint, we demonstrate that this direction-dependent stability can be attributed to two Mg clamps that cooperate and generate mechanical resistance in the pRNA’s coaxial direction. Our results suggest that the asymmetric nature of the 3WJ’s mechanical stability is entwined with its biological function: Enhanced rigidity along the portal axis is likely essential to withstand the strain caused by DNA condensation, and flexibility in other directions should aid in the assembly of the pRNA and its association with other motor components

Fermi-crossing Type-II Dirac fermions and topological surface states in NiTe2

Transition-metal dichalcogenides (TMDs) offer an ideal platform to experimentally realize Dirac fermions. However, typically these exotic quasiparticles are located far away from the Fermi level, limiting the contribution of Dirac-like carriers to the transport properties. Here we show that NiTe2 hosts both bulk Type-II Dirac points and topological surface states. The underlying mechanism is shared with other TMDs and based on the generic topological character of the Te p-orbital manifold. However, unique to NiTe2, a significant contribution of Ni d orbital states shifts the energy of the Type-II Dirac point close to the Fermi level. In addition, one of the topological surface states intersects the Fermi energy and exhibits a remarkably large spin splitting of 120 meV. Our results establish NiTe2 as an exciting candidate for next-generation spintronics devices

Frontiers in Pigment Cell and Melanoma Research

We identify emerging frontiers in clinical and basic research of melanocyte biology and its associated biomedical disciplines. We describe challenges and opportunities in clinical and basic research of normal and diseased melanocytes that impact current approaches to research in melanoma and the dermatological sciences. We focus on four themes: (1) clinical melanoma research, (2) basic melanoma research, (3) clinical dermatology, and (4) basic pigment cell research, with the goal of outlining current highlights, challenges, and frontiers associated with pigmentation and melanocyte biology. Significantly, this document encapsulates important advances in melanocyte and melanoma research including emerging frontiers in melanoma immunotherapy, medical and surgical oncology, dermatology, vitiligo, albinism, genomics and systems biology, epidemiology, pigment biophysics and chemistry, and evolution

T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable

HIV controllers (HCs) are individuals who can naturally control HIV infection, partially due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis that superior function of CD8+ T cells from HCs is encoded by their T cell receptors (TCRs). We compared the functional properties of immunodominant HIV-specific TCRs obtained from HLA-B*2705 HCs and chronic progressors (CPs) following expression in primary T cells. T cells transduced with TCRs from HCs and CPs showed equivalent induction of epitope-specific cytotoxicity, cytokine secretion, and antigen-binding properties. Transduced T cells comparably, albeit modestly, also suppressed HIV infection in vitro and in humanized mice. We also performed extensive molecular dynamics simulations that provided a structural basis for similarities in cytotoxicity and epitope cross-reactivity. These results demonstrate that the differential abilities of HIV-specific CD8+ T cells from HCs and CPs are not genetically encoded in the TCRs alone and must depend on additional factors

Towards better utilization of NEXRAD data in hydrology: An overview of hydro-NEXRAD

With a very modest investment in computer hardware and the open-source local data manger (LDM) software from UCAR\u27s Unidata Program Center, an individual researcher can receive a variety of NEXRAD Level III gridded rainfall products, and the unprocessed Level II data in real-time from most NEXRAD radars. Additionally, the National Climatic Data Center has vast archives of these products and Level II data. Still, significant obstacles remain in order to unlock the full potential of the data. One set of obstacles is related to effective management of multi-terabyte data sets: storing, compressing, and backing up. A second set of obstacles, for hydrologists and hydrometeorologists in particular, is that the NEXRAD Level III products are not well suited for application in hydrology. There is a strong need for the generation of high-quality products directly from the Level II data with well-documented steps that include quality control, removal of false echoes, rainfall estimation algorithms with variety of corrections, coordinate conversion and georeferencing, conversion to a convenient data format(s), and integration with GIS. For hydrologists it is imperative that these procedures are basin-centered as opposed to radar-centered. Thirdly, the amount of data present in a multi-year, multi-radar dataset is such that simple cataloging and indexing of the data is not sufficient. Rather, sophisticated metadata extraction and management techniques are required. The authors describe and discuss the Hydro-NEXRAD software system that addresses the above three challenges. With support from the National Science Foundation through its ITR program, the authors are developing a basin-centered framework for addressing all these issues in a comprehensive manner, tailored specifically for use of NEXRAD data in hydrology and hydrometeorology. Through a flexible web interface users can search a large metadata database base, managed by a relational database, for subsets of interest. Well-chosen and documented defaults are provided for the flow from unprocessed NEXRAD data to basin-centered rainfall estimates at a desired space-time resolution. In addition to the web interface, there are web services that provide access to scripts and compiled programs. © 2007 ASCE

Dynamic scaling for 2D superconductors, Josephson junction arrays and superfluids

The value of the dynamic critical exponent $z$ is studied for two-dimensional superconducting, superfluid, and Josephson Junction array systems in zero magnetic field via the Fisher-Fisher-Huse dynamic scaling. We find $z\simeq5.6\pm0.3$, a relatively large value indicative of non-diffusive dynamics. Universality of the scaling function is tested and confirmed for the thinnest samples. We discuss the validity of the dynamic scaling analysis as well as the previous studies of the Kosterlitz-Thouless-Berezinskii transition in these systems, the results of which seem to be consistent with simple diffusion ($z=2$). Further studies are discussed and encouraged.Comment: 19 pages in two-column RevTex, 8 embedded EPS figure

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells