Recognition of abasic sites and single base bulges in DNA by a metalloinsertor

Abasic sites and single base bulges are thermodynamically destabilizing DNA defects that can lead to cancerous transformations if left unrepaired by the cell. Here we discuss the binding properties with abasic sites and single base bulges of Rh(bpy)_2(chrysi)^(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)_2(chrysi)^(3+) selectively binds abasic sites with affinities of 1−4 × 10^6 M^(−1); specific binding is independent of unpaired base identity but is somewhat contingent on sequence context. Single base bulges are also selectively bound and cleaved, but in this case, the association constants are significantly lower (~10^5 M^(−1)), and the binding is dependent on both unpaired base identity and bulge sequence context. A wide variety of evidence, including strand scission asymmetry, binding enantiospecificity, and MALDI-TOF cleavage fragment analysis, suggests that Rh(bpy)_2(chrysi)^(3+) binds abasic sites, like mismatches, through insertion of the bulky chrysi ligand into the base pair stack from the minor groove side and ejection of the unpaired base. At single base bulge sites, a similar, though not identical, metalloinsertion mode is suggested. The recognition of abasic sites and single base bulges with bulky metalloinsertors holds promise for diagnostic and therapeutic applications

Recognition of DNA Base Pair Mismatches by a Cyclometalated Rh(III) Intercalator

Two cyclometalated complexes of Rh(III), rac-[Rh(ppy)_2chrysi]^+ and rac-[Rh(ppy)_2phi]^+, have been synthesized and characterized with respect to their binding to DNA. The structure of rac-[Rh(ppy)_2phi]Cl·H_2O·CH_2Cl_2 has been determined by X-ray diffraction (monoclinic, P2_1/c, Z = 4, a =18.447(3) Å, b = 9.770(1) Å, c = 17.661(3) Å, β = 94.821(11)°, V = 3172.0(8) Å^3) and reveals that the complex is a distorted octahedron with nearly planar ligands, similar in structure to the DNA mismatch recognition agent [Rh(bpy)_2chrysi]^(3+). The 2-phenylpyridyl nitrogen atoms are shown to be in the axial positions, as a result of trans-directing effects. This tendency simplifies the synthesis and purification of such complexes by limiting the number of possible isomers generated. The abilities of [Rh(ppy)_2chrysi]^+ and [Rh(ppy)_2phi]^+ to bind and, with photoactivation, to cleave DNA have been demonstrated in assays on duplex DNA in the absence and presence of a single CC mismatch. [Rh(ppy)_2chrysi]^+ was shown upon photoactivation to cleave DNA selectively at the base pair mismatch whereas [Rh(ppy)_2phi]^+ cleaves B-DNA nonspecifically. The reactivity of [Rh(ppy)_2chrysi]^+ was also compared to that of the known mismatch recognition agent [Rh(bpy)_2chrysi]^(3+). Competitive photocleavage studies revealed that a 14-fold excess of [Rh(ppy)_2chrysi]^+ was required to achieve the same level of binding as that of [Rh(bpy)_2chrysi]^(3+). However, the ratio of damage induced by [Rh(bpy)_2chrysi]^(3+) to that induced by [Rh(ppy)_2chrysi]^+ is considerably greater than this value, indicating that decreased photoefficiency for the cyclometalated complex must contribute to its significantly attenuated photoreactivity. These cyclometalated intercalators provide the starting points for the design of a new family of metal complexes targeted to DNA

Evaluation of segmentation algorithms for optical coherence tomography images of ovarian tissue

Ovarian cancer has the lowest survival rate among all gynecologic cancers predominantly due to late diagnosis. Early detection of ovarian cancer can increase 5-year survival rates from 40% up to 92%, yet no reliable early detection techniques exist. Optical coherence tomography (OCT) is an emerging technique that provides depth-resolved, high-resolution images of biological tissue in real-time and demonstrates great potential for imaging of ovarian tissue. Mouse models are crucial to quantitatively assess the diagnostic potential of OCT for ovarian cancer imaging; however, due to small organ size, the ovaries must first be separated from the image background using the process of segmentation. Manual segmentation is time-intensive, as OCT yields three-dimensional data. Furthermore, speckle noise complicates OCT images, frustrating many processing techniques. While much work has investigated noise-reduction and automated segmentation for retinal OCT imaging, little has considered the application to the ovaries, which exhibit higher variance and inhomogeneity than the retina. To address these challenges, we evaluate a set of algorithms to segment OCT images of mouse ovaries. We examine five preprocessing techniques and seven segmentation algorithms. While all preprocessing methods improve segmentation, Gaussian filtering is most effective, showing an improvement of 32 % ± 1.2 % . Of the segmentation algorithms, active contours performs best, segmenting with an accuracy of 94.8 % ± 1.2 % compared with manual segmentation. Even so, further optimization could lead to maximizing the performance for segmenting OCT images of the ovaries.National Science Foundation Graduate Research Fellowship Program [DGE-1143953]; National Institutes of Health/National Cancer Institute [1R01CA195723]; University of Arizona Cancer Center [3P30CA023074]This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Laser treatment of cutaneous vascular lesions

Methods for treating maladies such as cutaneous vascular lesions. A patient in need of vascular lesion treatment is identified. A hyperosmotic agent is administered to a region adjacent the lesion. Blood flow velocity is slowed within the region using the hyperosmotic agent, and the lesion is exposed to laser radiation.Board of Regents, University of Texas Syste

Functional muscle hypertrophy by increased insulin-like growth factor 1 does not require dysferlin.

IntroductionDysferlin loss-of-function mutations cause muscular dystrophy, accompanied by impaired membrane repair and muscle weakness. Growth promoting strategies including insulin-like growth factor 1 (IGF-1) could provide benefit but may cause strength loss or be ineffective. The objective of this study was to determine whether locally increased IGF-1 promotes functional muscle hypertrophy in dysferlin-null (Dysf-/- ) mice.MethodsMuscle-specific transgenic expression and postnatal viral delivery of Igf1 were used in Dysf-/- and control mice. Increased IGF-1 levels were confirmed by enzyme-linked immunosorbent assay. Testing for skeletal muscle mass and function was performed in male and female mice.ResultsMuscle hypertrophy occurred in response to increased IGF-1 in mice with and without dysferlin. Male mice showed a more robust response compared with females. Increased IGF-1 did not cause loss of force per cross-sectional area in Dysf-/- muscles.DiscussionWe conclude that increased local IGF-1 promotes functional hypertrophy when dysferlin is absent and reestablishes IGF-1 as a potential therapeutic for dysferlinopathies

Single- and multi-layer micro-scale diffractive lens fabrication for fiber imaging probes with versatile depth-of-field

Hair-thin optical fiber endoscopes have opened up new paradigms for advanced imaging applications in vivo. In certain applications, such as optical coherence tomography (OCT), light-shaping structures may be required on fiber facets to generate needle-like Bessel beams with large depth-of-field, while in others shorter depths of field with high lateral resolutions are preferable. In this paper, we demonstrate a novel method to fabricate light-shaping structures on optical fibres, achieved via bonding encapsulated planar diffractive lenses onto fiber facets. Diffractive metallic structures have the advantages of being simple to design, fabricate and transfer, and our encapsulation approach is scalable to multi-layer stacks. As a demonstration, we design and transfer a Fresnel zone plate and a diffractive axicon onto fiber facets, and show that the latter device generates a needle-like Bessel beam with 350 mu m focal depth. We also evaluate the imaging performance of both devices and show that the axicon fiber is able to maintain focussed images of a USAF resolution target over a 150 mu m distance. Finally, we fabricate a two-layer stack of Fresnel zone plates on a fiber and characterise the modified beam profile and demonstrate good imaging performance. We anticipate our fabrication approach could enable multi-functional complex optical structures (e.g. using plasmonics, polarization control) to be integrated onto fibers for ultra-thin advanced imaging and sensing

Targeting Abasic Sites and Single Base Bulges in DNA with Metalloinsertors

The site-specific recognition of abasic sites and single base bulges in duplex DNA by sterically expansive rhodium metalloinsertors has been investigated. Through DNA photocleavage experiments, Rh(bpy)_2(chrysi)^(3+) is shown to bind both abasic sites and single base bulges site-specifically and, upon irradiation, to cleave the backbone of the defect-containing DNA. Photocleavage titrations reveal that the metal complex binds DNA containing an abasic site with high affinity (2.6(5) × 10^6 M^(−1)), comparably to the metalloinsertor and a CC mismatch. The complex binds single base bulge sites with lower affinity (∼10^5 M^(−1)). Analysis of cleavage products and the correlation of affinities with helix destabilization suggest that Rh(bpy)_2(chrysi)^(3+) binds both lesions via metalloinsertion, as observed for Rh binding at mismatched sites, a binding mode in which the mismatched or unpaired bases are extruded from the helix and replaced in the base stack by the sterically expansive ligand of the metalloinsertor

Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow, and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has limited cross-disciplinary learning and research in important areas of ecosystem and community ecology. Here we expound on the “necrobiome” concept and develop a framework describing the decomposer communities and their interactions associated with plant and animal resource types within multiple ecosystems.We outline the biotic structure and ecological functions of the necrobiome, along with how the necrobiome fits into a broader landscape and ecosystem context. The expanded necrobiome model provides a set of perspectives on decomposer communities across resource types, and conceptually unifies plant and animal decomposer communities into the same framework, while acknowledging key differences in processes and mechanisms. This framework is intended to raise awareness among researchers, and advance the construction of explicit, mechanistic hypotheses that further our understanding of decomposer community contributions to biodiversity, the structure and function of ecosystems, global nutrient recycling and energy flow

NECROBIOME FRAMEWORK FOR BRIDGING DECOMPOSITION ECOLOGY OF AUTOTROPHICALLY AND HETEROTROPHICALLY DERIVED ORGANIC MATTER

Life arises from death through species that decompose dead biomass or necromass. This paper provides a synthesis of the species responsible for dead plant and animal decomposition and describes a conceptual perspective—the “necrobiome”— that defines the diverse and complex communities that interact to recycle necromass. The concept brings unification to the previously disparate fields of plant and animal decomposition by discussing the universal processes occurring across all forms of necromass. It highlights the factors that make each form of dead biomass different in a way that defines how unique necrobiomes drive decomposition and ultimately shape ecosystem structure and function