Biophysical Measurements of Cells, Microtubules, and DNA with an Atomic Force Microscope

Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here we review several AFM platforms (Dimension 3000 by Digital Instruments, EasyScan2 by Nanosurf, ezAFM by Nanomagnetics, and TKAFM by Thorlabs) and describe various biophysical experiments that could be done in the teaching laboratory using these instruments. In particular, we focus on experiments that image biological materials and quantify biophysical parameters: 1) imaging cells to determine membrane tension, 2) imaging microtubules to determine their persistence length, 3) imaging the random walk of DNA molecules to determine their contour length, and 4) imaging stretched DNA molecules to measure the tensional force.Comment: 29 page preprint, 7 figures, 1 tabl

Patterns of social determinants of health associated with drug use among women living with HIV in Canada: a latent class analysis

Background and AimsIdentifying typologies of social determinants of health (SDoH) vulnerability influencing drug use practices among women living with HIV (WLWH) can help to address associated harms. This research aimed to explore the association of SDoH clusters with drug use among WLWH.DesignLatent class analysis (LCA) was used to identify the distinct clusters of SDoH. Inverse probability weighting (IPW) was employed to account for confounding and potential selection bias. Associations were analyzed using generalized linear model with log link and Poisson distribution, and then weighted risk ratio (RR) and 95% confidence intervals (CI) were reported.Setting and ParticipantsData from 1422 WLWH recruited at timeâ point 1 of the Canadian HIV Women’s Sexual and Reproductive Health Cohort Study (CHIWOS, 2013â 15), with 1252 participants at 18 months followâ up (timeâ point 2).MeasurementsDrug use was defined as use of illicit/nonâ prescribed opioids/stimulants in the past 6 months. SDoH indicators included: race discrimination, gender discrimination, HIV stigma, social support, access to care, food security, income level, employment status, education, housing status and histories of recent sex work and incarceration.FindingsLCA identified four SDoH classes: no/least SDoH adversities (6.6%), discrimination/stigma (17.7%), economic hardship (30.8%) and most SDoH adversities (45.0%). Drug use was reported by 17.5% and 17.2% at timeâ points 1 and 2, respectively. WLWH with no/least SDoH adversities were less likely to report drug use than those in economic hardship class (weighted RR = 0.13; 95% CIs = 0.03, 0.63), discrimination/stigma class (weighted RR = 0.15; 95% CIs = 0.03, 0.78), and most SDoH adversities class (weighted RR = 0.13; 95% CIs = 0.03, 0.58).ConclusionsSocial determinants of health vulnerabilities are associated with greater likelihood of drug use, underscoring the significance of addressing interlinked social determinants and drug use through the course of HIV care and treatment.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149504/1/add14566_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149504/2/add14566.pd

The targeted delivery of multicomponent cargos to cancer cells by nanoporous particle-supported lipid bilayers.

Encapsulation of drugs within nanocarriers that selectively target malignant cells promises to mitigate side effects of conventional chemotherapy and to enable delivery of the unique drug combinations needed for personalized medicine. To realize this potential, however, targeted nanocarriers must simultaneously overcome multiple challenges, including specificity, stability and a high capacity for disparate cargos. Here we report porous nanoparticle-supported lipid bilayers (protocells) that synergistically combine properties of liposomes and nanoporous particles. Protocells modified with a targeting peptide that binds to human hepatocellular carcinoma exhibit a 10,000-fold greater affinity for human hepatocellular carcinoma than for hepatocytes, endothelial cells or immune cells. Furthermore, protocells can be loaded with combinations of therapeutic (drugs, small interfering RNA and toxins) and diagnostic (quantum dots) agents and modified to promote endosomal escape and nuclear accumulation of selected cargos. The enormous capacity of the high-surface-area nanoporous core combined with the enhanced targeting efficacy enabled by the fluid supported lipid bilayer enable a single protocell loaded with a drug cocktail to kill a drug-resistant human hepatocellular carcinoma cell, representing a 10(6)-fold improvement over comparable liposomes

Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales

A Long-Term Vision for an Ecologically Sound Platte River

The Platte River extends about 310 mi (499 km) from North Platte, Nebraska, to its terminus at the Missouri River confluence near Plattsmouth, Nebraska. The Platte River Valley is a continentally significant ecosystem that serves as a major stopover for migratory waterbirds in the Central Flyway including the endangered Whooping Crane (Grus americana) and \u3e1 million Sandhill Cranes (Antigone canadensis) at the peak of spring migration. However, the Platte River Valley also supports a great diversity of avifauna including grassland breeding birds, native stream fish, vascular plants, herpetofauna, mammals, pollinators, and aquatic macroinvertebrates. Despite ongoing conservation efforts since the mid-1970s the ecosystem remains largely conservation dependent and an increasing number of species across taxa are being considered at risk of regional extirpation or outright extinction. However, given the attention provided to conservation in the Platte River Valley and the need to maintain ecologically functional stopover sites in the Central Flyway, there is a great opportunity to create a resilient refugium for biodiversity conservation in the central Great Plains. To that end we convened a working group of \u3e18 individuals representing \u3e9 organizations including representatives from non-profit conservation organizations, universities, and state and federal natural resource agencies to develop a long-term vision for an ecologically sound Platte River Valley (PRV). We met in groups of varying size for \u3e170 hours throughout a more than 3-year period and developed conservation priorities and objectives using a landscape design process. Landscape design is an interdisciplinary conservation planning process that incorporates components of landscape ecology and social dimensions of natural resources with the explicit intention of improving conservation implementation.https://digitalcommons.unl.edu/zeabook/1128/thumbnail.jp

Ca2+-Dependent Phosphorylation of RyR2 Can Uncouple Channel Gating from Direct Cytosolic Ca2+ Regulation

Phosphorylation of the cardiac ryanodine receptor (RyR2) is thought to be important not only for normal cardiac excitation-contraction coupling but also in exacerbating abnormalities in Ca2+ homeostasis in heart failure. Linking phosphorylation to specific changes in the single-channel function of RyR2 has proved very difficult, yielding much controversy within the field. We therefore investigated the mechanistic changes that take place at the single-channel level after phosphorylating RyR2 and, in particular, the idea that PKA-dependent phosphorylation increases RyR2 sensitivity to cytosolic Ca2+. We show that hyperphosphorylation by exogenous PKA increases open probability (Po) but, crucially, RyR2 becomes uncoupled from the influence of cytosolic Ca2+; lowering [Ca2+] to subactivating levels no longer closes the channels. Phosphatase (PP1) treatment reverses these gating changes, returning the channels to a Ca2+-sensitive mode of gating. We additionally found that cytosolic incubation with Mg2+/ATP in the absence of exogenously added kinase could phosphorylate RyR2 in approximately 50% of channels, thereby indicating that an endogenous kinase incorporates into the bilayer together with RyR2. Channels activated by the endogenous kinase exhibited identical changes in gating behavior to those activated by exogenous PKA, including uncoupling from the influence of cytosolic Ca2+. We show that the endogenous kinase is both Ca2+-dependent and sensitive to inhibitors of PKC. Moreover, the Ca2+-dependent, endogenous kinase–induced changes in RyR2 gating do not appear to be related to phosphorylation of serine-2809. Further work is required to investigate the identity and physiological role of this Ca2+-dependent endogenous kinase that can uncouple RyR2 gating from direct cytosolic Ca2+ regulation

Searching for gravitational waves from known pulsars

We present upper limits on the amplitude of gravitational waves from 28 isolated pulsars using data from the second science run of LIGO. The results are also expressed as a constraint on the pulsars' equatorial ellipticities. We discuss a new way of presenting such ellipticity upper limits that takes account of the uncertainties of the pulsar moment of inertia. We also extend our previous method to search for known pulsars in binary systems, of which there are about 80 in the sensitive frequency range of LIGO and GEO 600.Comment: Accepted by CQG for the proceeding of GWDAW9, 7 pages, 2 figure

On the Search For Transits of the Planets Orbiting Gl 876

We report the results of a globally coordinated photometric campaign to search for transits by the P ~ 30 d and P ~ 60 d outer planets of the 3-planet system orbiting the nearby M-dwarf Gl 876. These two planets experience strong mutual perturbations, which necessitate use of a dynamical (four-body) model to compute transit ephemerides for the system. Our photometric data have been collected from published archival sources, as well as from our photometric campaigns that were targeted to specific transit predictions. Our analysis indicates that transits by planet "c" (P ~ 30 d) do not currently occur, in concordance with the best-fit i = 50 degree co-planar configuration obtained by dynamical fits to the most recent radial velocity data for the system. Transits by planet "b" (P ~ 60 d) are not entirely ruled out by our observations, but our data indicate that it is very unlikely that they occur. Our experience with the Gl 876 system suggests that a distributed ground-based network of small telescopes can be used to search for transits of very low mass M-stars by terrestrial-sized planets.Comment: currently 17pp w/Figs, 10 figures; to appear in Astrophysical Journal article December 2006 v653n