Stick index of knots and links in the cubic lattice

The cubic lattice stick index of a knot type is the least number of sticks necessary to construct the knot type in the 3-dimensional cubic lattice. We present the cubic lattice stick index of various knots and links, including all (p,p+1)-torus knots, and show how composing and taking satellites can be used to obtain the cubic lattice stick index for a relatively large infinite class of knots. Additionally, we present several bounds relating cubic lattice stick index to other known invariants.Comment: 16 pages, 12 figure

Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer's disease model.

Many risk genes for the development of Alzheimer's disease (AD) are exclusively or highly expressed in myeloid cells. Microglia are dependent on colony-stimulating factor 1 receptor (CSF1R) signaling for their survival. We designed and synthesized a highly selective brain-penetrant CSF1R inhibitor (PLX5622) allowing for extended and specific microglial elimination, preceding and during pathology development. We find that in the 5xFAD mouse model of AD, plaques fail to form in the parenchymal space following microglial depletion, except in areas containing surviving microglia. Instead, Aβ deposits in cortical blood vessels reminiscent of cerebral amyloid angiopathy. Altered gene expression in the 5xFAD hippocampus is also reversed by the absence of microglia. Transcriptional analyses of the residual plaque-forming microglia show they exhibit a disease-associated microglia profile. Collectively, we describe the structure, formulation, and efficacy of PLX5622, which allows for sustained microglial depletion and identify roles of microglia in initiating plaque pathogenesis

Positive ecological interactions and the success of seagrass restoration

Seagrasses provide multiple ecosystem services including nursery habitat, improved water quality, coastal protection, and carbon sequestration. However, seagrasses are in crisis as global coverage is declining at an accelerating rate. With increased focus on ecological restoration as a conservation strategy, methods that enhance restoration success need to be explored. Decades of work in coastal plant ecosystems, including seagrasses, has shown that positive species relationships and feedbacks are critical for ecosystem stability, expansion, and recovery from disturbance. We reviewed the restoration literature on seagrasses and found few studies have tested for the beneficial effects of including positive species interactions in seagrass restoration designs. Here we review the full suite of positive species interactions that have been documented in seagrass ecosystems, where they occur, and how they might be integrated into seagrass restoration. The few studies in marine plant communities that have explicitly incorporated positive species interactions and feedbacks have found an increase in plant growth with little additional resource investment. As oceans continue to change and stressors become more prevalent, harnessing positive interactions between species through innovative approaches will likely become key to successful seagrass restoration

Positive Ecological Interactions and the Success of Seagrass Restoration

Seagrasses provide multiple ecosystem services including nursery habitat, improved water quality, coastal protection, and carbon sequestration. However, seagrasses are in crisis as global coverage is declining at an accelerating rate. With increased focus on ecological restoration as a conservation strategy, methods that enhance restoration success need to be explored. Decades of work in coastal plant ecosystems, including seagrasses, has shown that positive species relationships and feedbacks are critical for ecosystem stability, expansion, and recovery from disturbance. We reviewed the restoration literature on seagrasses and found few studies have tested for the beneficial effects of including positive species interactions in seagrass restoration designs. Here we review the full suite of positive species interactions that have been documented in seagrass ecosystems, where they occur, and how they might be integrated into seagrass restoration. The few studies in marine plant communities that have explicitly incorporated positive species interactions and feedbacks have found an increase in plant growth with little additional resource investment. As oceans continue to change and stressors become more prevalent, harnessing positive interactions between species through innovative approaches will likely become key to successful seagrass restoration

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

MicroRNAs (miRNAs) are prevalent regulatory RNAs that mediate gene silencing and play key roles in diverse cellular processes. While synthetic RNA-based regulatory systems that integrate regulatory and sensing functions have been demonstrated, the lack of detail on miRNA structure–function relationships has limited the development of integrated control systems based on miRNA silencing. Using an elucidated relationship between Drosha processing and the single-stranded nature of the miRNA basal segments, we developed a strategy for designing ligand-responsive miRNAs. We demonstrate that ligand binding to an aptamer integrated into the miRNA basal segments inhibits Drosha processing, resulting in titratable control over gene silencing. The generality of this control strategy was shown for three aptamer–small molecule ligand pairs. The platform can be extended to the design of synthetic miRNAs clusters, cis-acting miRNAs and self-targeting miRNAs that act both in cis and trans, enabling fine-tuning of the regulatory strength and dynamics. The ability of our ligand-responsive miRNA platform to respond to user-defined inputs, undergo regulatory performance tuning and display scalable combinatorial control schemes will help advance applications in biological research and applied medicine

Epigenetic effects of metformin: From molecular mechanisms to clinical implications

There is a growing body of evidence that links epigenetic modifications to type 2 diabetes. Researchers have more recently investigated effects of commonly used medications, including those prescribed for diabetes, on epigenetic processes. This work reviews the influence of the widely used antidiabetic drug metformin on epigenomics, microRNA levels and subsequent gene expression, and potential clinical implications. Metformin may influence the activity of numerous epigenetic modifying enzymes, mostly by modulating the activation of AMP-activated protein kinase (AMPK). Activated AMPK can phosphorylate numerous substrates, including epigenetic enzymes such as histone acetyltransferases (HATs), class II histone deacetylases (HDACs) and DNA methyltransferases (DNMTs), usually resulting in their inhibition; however, HAT1 activity may be increased. Metformin has also been reported to decrease expression of multiple histone methyltransferases, to increase the activity of the class III HDAC SIRT1 and to decrease the influence of DNMT inhibitors. There is evidence that these alterations influence the epigenome and gene expression, and may contribute to the antidiabetic properties of metformin and, potentially, may protect against cancer, cardiovascular disease, cognitive decline and aging. The expression levels of numerous microRNAs are also reportedly influenced by metformin treatment and may confer antidiabetic and anticancer activities. However, as the reported effects of metformin on epigenetic enzymes act to both increase and decrease histone acetylation, histone and DNA methylation, and gene expression, a significant degree of uncertainty exists concerning the overall effect of metformin on the epigenome, on gene expression, and on the subsequent effect on the health of metformin users

Change in Markers of Bone Metabolism with Chemotherapy for Advanced Prostate Cancer: Interleukin-6 Response Is a Potential Early Indicator of Response to Therapy

Men with androgen-independent prostate cancer (AIPC) frequently have bone metastasis. The effects of chemotherapy on markers of bone metabolism have not been well characterized. We conducted a prospective study of patients with AIPC randomized in the first cycle to receive either docetaxel/estramustine or zoledronic acid, a bisphosphonate, to inhibit osteoclastic activity. Here we report the effects of therapy on markers of bone metabolism in these patients following the first cycle of therapy. Serum levels of several indices of bone remodeling were evaluated using commercial enzyme-linked immunosorbent assays. Changes in markers of bone metabolism were compared in patients receiving initial chemotherapy versus bisphosphonate. There was no significant difference in median change in any of the measured bone markers in patients given zoledronic acid when compared to chemotherapy. When comparing responders to nonresponders, overall interleukin-6 (IL-6) decreased by 35% in prostate-specific antigen responders; whereas, IL-6 levels increased by 76% in nonresponders (p = 0.03). Elevated IL-6 levels and reductions in IL-6 levels early in treatment may reflect ultimate clinical response to docetaxel-based regimens.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78145/1/jir.2008.0024.pd

Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation

Improved diagnostic methods are needed for bronchiolitis obliterans syndrome (BOS), a serious complication after allogeneic hematopoietic cell transplantation (HCT) and lung transplantation. For proteins candidate discovery, we compared plasma pools from HCT transplantation recipients with: BOS at onset (n=12), pulmonary infection (n=16), chronic graft-versus-host disease without pulmonary involvement (n=15), and no chronic complications post-HCT (n=15). Pools were labeled with different tags [isobaric Tags for Relative and Absolute Quantification (iTRAQ)], and two software tools identified differentially expressed proteins (≥1.5-fold change). Candidate proteins were further selected using a six-step computational biology approach. The diagnostic value of the lead candidate, matrix metalloproteinase-3 (MMP-3), was evaluated by ELISA in plasma of a verification cohort (n=112) with and without BOS following HCT (n=76) or lung transplantation (n=36). MMP-3 plasma concentrations differed significantly between patients with and without BOS (AUC=0.77). Thus, MMP-3 represents a potential non-invasive blood test for diagnosis of BOS

DNA-Controlled Excitonic Switches

Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function

HDAC9 is implicated in atherosclerotic aortic calcification and affects vascular smooth muscle cell phenotype.

Aortic calcification is an important independent predictor of future cardiovascular events. We performed a genome-wide association meta-analysis to determine SNPs associated with the extent of abdominal aortic calcification (n = 9,417) or descending thoracic aortic calcification (n = 8,422). Two genetic loci, HDAC9 and RAP1GAP, were associated with abdominal aortic calcification at a genome-wide level (P < 5.0 × 10-8). No SNPs were associated with thoracic aortic calcification at the genome-wide threshold. Increased expression of HDAC9 in human aortic smooth muscle cells promoted calcification and reduced contractility, while inhibition of HDAC9 in human aortic smooth muscle cells inhibited calcification and enhanced cell contractility. In matrix Gla protein-deficient mice, a model of human vascular calcification, mice lacking HDAC9 had a 40% reduction in aortic calcification and improved survival. This translational genomic study identifies the first genetic risk locus associated with calcification of the abdominal aorta and describes a previously unknown role for HDAC9 in the development of vascular calcification