The Role of Esterification on Detection of Protonated and Deprotonated Peptide Ions in Matrix Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry (MS)

Esterification was used to investigate how introduction of aliphatic chains within the peptide structure affects the MALDI response of ions analyzed in both polarity regimes. In binary mixtures containing equimolar amounts of a peptide with its correspondent alkyl ester, derivatization of the carboxylic groups has the tendency to increase MALDI detection of the modified protonated peptide ions. This positive effect on ion yield is more pronounced when longer alcohols are employed. In negative mode, the situation is antithetic and esterification produces a deleterious effect on the ion yield of the corresponding deprotonated species. From the data reported here we postulate that modifications of the acidic character of peptides prevent formation of anionic species under MALDI analysis. Furthermore, suppression of the formation pathway for anions alters the overall number of molecules which can undergo protonation. This results in an increased ion yield for the protonated esters

Positive and Negative Regulatory Elements in the HIV-1 5'UTR Control Specific Recognition by Gag

Biological Sciences (The Ohio State University Denman Undergraduate Research Forum)The 5ʹ untranslated region (5ʹUTR) of the human immunodeficiency virus type 1 (HIV-1) genomic RNA (gRNA) contains a structured RNA element (termed Psi) that is specifically recognized by the HIV-1 Gag polyprotein, ensuring that two strands of gRNA are packaged into newly assembled virions. However, the mechanism by which Gag recognizes gRNA over other cellular RNAs and spliced viral RNAs is not well understood. A recent study suggested that a negative regulatory element upstream of Psi reduces high-affinity Gag binding, and a positive regulatory element downstream of Psi counteracts the upstream element and restores high-affinity binding. The aim of this study is to determine how these elements affect the specificity and mode of Gag binding. Using a fluorescence anisotropy-based salt-titration binding assay, the electrostatic and nonelectrostatic (i.e., specific) components of binding were measured. We have previously shown that Gag interacts with a 109-nucleotide (nt) Psi RNA construct that lacks the putative regulatory elements with high specificity and relatively few electrostatic interactions. Using a 356-nt RNA construct that includes the negative regulatory element in addition to Psi, we observed a loss in Gag binding specificity and an increase in electrostatic interactions. Interestingly, a 400-nt construct that contains the positive and negative elements flanking Psi restored highly specific binding and reduced the electrostatic interactions made with the RNA. Furthermore, a construct wherein the 40-nt positive regulatory element was appended to Psi, demonstrated the same specificity as Psi alone. Taken together, these data are consistent with a mechanism whereby the negative and positive regulatory elements flanking Psi modulate Gag binding mode and specificity.Undergraduate Education Summer Research FellowshipArts & Sciences Undergraduate Research ScholarshipSOLAR Research GrantNo embargoAcademic Major: Biochemistr

Development of a Low-Cost 6 DOF Brick Tracking System for Use in Advanced Gas-Cooled Reactor Model Tests

This paper presents the design of a low-cost, compact instrumentation system to enable six degree of freedom motion tracking of acetal bricks within an experimental model of a cracked Advanced Gas-Cooled Reactor (AGR) core. The system comprises optical and inertial sensors and capitalises on the advantages offered by data fusion techniques. The optical system tracks LED indicators, allowing a brick to be accurately located even in cluttered images. The LED positions are identified using a geometrical correspondence algorithm, which was optimised to be computationally efficient for shallow movements, and complex camera distortions are corrected using a versatile Incident Ray-Tracking calibration. Then, a Perspective-Ray-based Scaled Orthographic projection with Iteration (PRSOI) algorithm is applied to each LED position to determine the six degree of freedom pose. Results from experiments show that the system achieves a low Root Mean Squared (RMS) error of 0.2296 mm in x, 0.3943 mm in y, and 0.0703 mm in z. Although providing an accurate measurement solution, the optical tracking system has a low sample rate and requires the line of sight to be maintained throughout each test. To increase the robustness, accuracy, and sampling frequency of the system, the optical system can be augmented with an Inertial Measurement Unit (IMU). This paper presents a method to integrate the optical system and IMU data by accurately timestamping data from each set of sensors and aligning the two coordinate axes. Once miniaturised, the developed system will be used to track smaller components within the AGR models that cannot be tracked with current instrumentation, expanding reactor core modelling capabilities

Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals

Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals

Timoshenko Bending and Eshelby Twisting Predicted in Molecular Nanocrystals

Well-formed crystals are polyhedral with flat facets and sharp edges. Nevertheless, a remarkable number of molecular crystals can bend and twist during growth. Many others can be distorted by applying external forces or creating heterogeneities by temperature gradient or photochemical reaction. As part of an effort to identify the forces that so commonly deform molecular crystals and to characterize their consequences, a force field is evaluated for its ability to predict mechanical distortions in nanocrystals. Macroscopic materials provide estimates of the expected responses that were tested here in silico for "molecular bimetallic strips" created from rods of iodoform and bromoform in smooth contact and nanocrystalline rods of iodoform with left and right screw dislocations. It was demonstrated that an optimized force field based largely on AMBER parameters matches expectations for elastic and plastic distortions, despite the fact that these mechanical responses are far removed from the force field parametrization set

A network model for field and quenched disorder effects in artificial spin ice

We have performed a systematic study of the effects of field strength and quenched disorder on the driven dynamics of square artificial spin ice. We construct a network representation of the configurational phase space, where nodes represent the microscopic configurations and a directed link between node i and node j means that the field may induce a transition between the corresponding configurations. In this way, we are able to quantitatively describe how the field and the disorder affect the connectedness of states and the reversibility of dynamics. In particular, we have shown that for optimal field strengths, a substantial fraction of all states can be accessed using external driving fields, and this fraction is increased by disorder. We discuss how this relates to control and potential information storage applications for artificial spin ices

Megakaryocytes promote murine osteoblastic HSC niche expansion and stem cell engraftment after radioablative conditioning

Successful hematopoietic stem cell (HSC) transplantation requires donor HSC engraftment within specialized bone marrow microenvironments known as HSC niches. We have previously reported a profound remodeling of the endosteal osteoblastic HSC niche after total body irradiation (TBI), defined as relocalization of surviving megakaryocytes to the niche site and marked expansion of endosteal osteoblasts. We now demonstrate that host megakaryocytes function critically in expansion of the endosteal niche after preparative radioablation and in the engraftment of donor HSC. We show that TBI-induced migration of megakaryocytes to the endosteal niche depends on thrombopoietin signaling through the c-MPL receptor on megakaryocytes, as well as CD41 integrin-mediated adhesion. Moreover, niche osteoblast proliferation post-TBI required megakaryocyte-secreted platelet-derived growth factor-BB. Furthermore, blockade of c-MPL-dependent megakaryocyte migration and function after TBI resulted in a significant decrease in donor HSC engraftment in primary and competitive secondary transplantation assays. Finally, we administered thrombopoietin to mice beginning 5 days before marrow radioablation and ending 24 hours before transplant to enhance megakaryocyte function post-TBI, and found that this strategy significantly enhanced donor HSC engraftment, providing a rationale for improving hematopoietic recovery and perhaps overall outcome after clinical HSC transplantation.Successful hematopoietic stem cell (HSC) transplantation requires donor HSC engraftment within specialized bone marrow microenvironments known as HSC niches. We have previously reported a profound remodeling of the endosteal osteoblastic HSC niche after total body irradiation (TBI), defined as relocalization of surviving megakaryocytes to the niche site and marked expansion of endosteal osteoblasts. We now demonstrate that host megakaryocytes function critically in expansion of the endosteal niche after preparative radioablation and in the engraftment of donor HSC. We show that TBI-induced migration of megakaryocytes to the endosteal niche depends on thrombopoietin signaling through the c-MPL receptor on megakaryocytes, as well as CD41 integrin-mediated adhesion. Moreover, niche osteoblast proliferation post-TBI required megakaryocyte-secreted platelet-derived growth factor-BB. Furthermore, blockade of c-MPL-dependent megakaryocyte migration and function after TBI resulted in a significant decrease in donor HSC engraftment in primary and competitive secondary transplantation assays. Finally, we administered thrombopoietin to mice beginning 5 days before marrow radioablation and ending 24 hours before transplant to enhance megakaryocyte function post-TBI, and found that this strategy significantly enhanced donor HSC engraftment, providing a rationale for improving hematopoietic recovery and perhaps overall outcome after clinical HSC transplantation

IGF-1-mediated osteoblastic niche expansion enhances long-term hematopoietic stem cell engraftment after murine bone marrow transplantation

The efficiency of hematopoietic stem cell (HSC) engraftment after bone marrow (BM) transplantation depends largely on the capacity of the marrow microenvironment to accept the transplanted cells. While radioablation of BM damages osteoblastic stem cell niches, little is known about their restoration and mechanisms governing their receptivity to engraft transplanted HSCs. We previously reported rapid restoration and profound expansion of the marrow endosteal microenvironment in response to marrow radioablation. Here, we show that this reorganization represents proliferation of mature endosteal osteoblasts which seem to arise from a small subset of high-proliferative, relatively radio-resistant endosteal cells. Multiple layers of osteoblasts form along the endosteal surface within 48 hours after total-body irradiation, concomitant with a peak in marrow cytokine expression. This niche reorganization fosters homing of the transplanted hematopoietic cells to the host marrow space and engraftment of long-term (LT)-HSC. Inhibition of insulin-like growth factor (IGF)-1-receptor tyrosine kinase signaling abrogates endosteal osteoblast proliferation and donor HSC engraftment, suggesting that the cytokine IGF-1 is a crucial mediator of endosteal niche reorganization and consequently donor HSC engraftment. Further understanding of this novel mechanism of IGF-1-dependent osteoblastic niche expansion and HSC engraftment may yield clinical applications for improving engraftment efficiency after clinical HSC transplantation.The efficiency of hematopoietic stem cell (HSC) engraft-ment after bone marrow (BM) transplantation depends largely on the capacity of the marrow microenvironment to accept the transplanted cells. While radioablation of BM damages osteoblastic stem cell niches, little is known about their restoration and mechanisms governing their receptivity to engraft transplanted HSCs. We previously reported rapid restoration and profound expansion of the marrow endosteal microenvironment in response to marrow radioablation. Here, we show that this reorganization represents proliferation of mature endosteal osteoblasts which seem to arise from a small subset of high-proliferative, relatively radio-resistant endosteal cells. Multiple layers of osteoblasts form along the endosteal surface within 48 hours after total body irradiation, concomitant with a peak in marrow cytokine expression. This niche reorganization fosters homing of the transplanted hematopoietic cells to the host marrow space and engraft-ment of long-term-HSC. Inhibition of insulin-like growth factor (IGF)-1-receptor tyrosine kinase signaling abrogates endosteal osteoblast proliferation and donor HSC engraft-ment, suggesting that the cytokine IGF-1 is a crucial mediator of endosteal niche reorganization and consequently donor HSC engraftment. Further understanding of this novel mechanism of IGF-1-dependent osteoblastic niche expansion and HSC engraftment may yield clinical applications for improving engraftment efficiency after clinical HSC transplantation. © AlphaMed Press

Delayed marrow infusion in mice enhances hematopoietic and osteopoietic engraftment by facilitating transient expansion of the osteoblastic niche

Transplantation of bone marrow cells leads to engraftment of osteopoietic and hematopoietic progenitors. We sought to determine whether the recently described transient expansion of the host osteoblastic niche after marrow radioablation promotes engraftment of both osteopoietic and hematopoietic progenitor cells. Mice infused with marrow cells 24 hours after total body irradiation (TBI) demonstrated significantly greater osteopoietic and hematopoietic progenitor chimerism than did mice infused at 30 minutes or 6 hours. Irradiated mice with a lead shield over 1 hind limb showed greater hematopoietic chimerism in the irradiated limb than in the shielded limb at both the 6- and 24-hour intervals. By contrast, the osteopoietic chimerism was essentially equal in the 2 limbs at each of these intervals, although it significantly increased when cells were infused 24 hours compared with 6 hours after TBI. Similarly, the number of donor phenotypic long-term hematopoietic stem cells was equivalent in the irradiated and shielded limbs after each irradiation-to-infusion interval but was significantly increased at the 24-hour interval. Our findings indicate that a 24-hour delay in marrow cell infusion after TBI facilitates expansion of the endosteal osteoblastic niche, leading to enhanced osteopoietic and hematopoietic engraftment.Transplantation of bone marrow cells leads to engraftment of osteopoietic and hematopoietic progenitors. We sought to determine whether the recently described transient expansion of the host osteoblastic niche after marrow radioablation promotes engraftment of both osteopoietic and hematopoietic progenitor cells. Mice infused with marrow cells 24hours after total body irradiation (TBI) demonstrated significantly greater osteopoietic and hematopoietic progenitor chimerism than did mice infused at 30minutes or 6hours. Irradiated mice with a lead shield over 1 hind limb showed greater hematopoietic chimerism in the irradiated limb than in the shielded limb at both the 6- and 24-hour intervals. By contrast, the osteopoietic chimerism was essentially equal in the 2 limbs at each of these intervals, although it significantly increased when cells were infused 24hours compared with 6hours after TBI. Similarly, the number of donor phenotypic long-term hematopoietic stem cells was equivalent in the irradiated and shielded limbs after each irradiation-to-infusion interval but was significantly increased at the 24-hour interval. Our findings indicate that a 24-hour delay in marrow cell infusion after TBI facilitates expansion of the endosteal osteoblastic niche, leading to enhanced osteopoietic and hematopoietic engraftment. © 2013