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

Monitoring Soil Quality to Assess the Sustainability of Harvesting Corn Stover

Harvesting feedstock for biofuel production must not degrade soil, water, or air resources. Our objective is to provide an overview of field research being conducted to quantify effects of harvesting corn (Zea mays L.) stover as a bioenergy feedstock. Coordinated field studies are being conducted near Ames, IA; St. Paul and Morris, MN; Mead, NE; University Park, PA; Florence, SC; and Brookings, SD., as part of the USDA-ARS Renewable Energy Assessment Project (REAP). A baseline soil quality assessment was made using the Soil Management Assessment Framework (SMAF). Corn grain and residue yield for two different stover harvest rates (∼50% and ∼90%) are being measured. Available soil data remains quite limited but sufficient for an initial SMAF analysis that confirms total organic carbon (TOC) is a soil quality indicator that needs to be closely monitored closely to quantify crop residue removal effects. Overall, grain yields averaged 9.7 and 11.7 Mg ha−1 (155 and 186 bu acre−1) in 2008 and 2009, values that are consistent with national averages for both years. The average amount of stover collected for the 50% treatment was 2.6 and 4.2 Mg ha−1 for 2008 and 2009, while the 90% treatment resulted in an average removal of 5.4 and 7.4 Mg ha−1, respectively. Based on a recent literature review, both stover harvest scenarios could result in a gradual decline in TOC. However, the literature value has a large standard error, so continuation of this long-term multi-location study for several years is warranted

International Society of Nephrology Global Kidney Health Atlas: structures, organization, and services for the management of kidney failure in the Middle East

Kidney failure is the permanent impairment of kidney function associated with increased morbidity, hospitalization, and requirement for kidney replacement therapy. A total of 11 countries in the Middle East region (84.6) responded to the survey. The prevalence of chronic kidney disease in the region ranged from 5.2 to 10.6, whereas prevalence of treated kidney failure ranged from 152 to 826 per million population. Overall, the incidence of kidney transplantation was highest in Iran (30.9 per million population) and lowest in Oman and the United Arab Emirates (2.2 and 3.0 per million population, respectively). Long-term hemodialysis services were available in all countries, long-term peritoneal dialysis services were available in 9 (69.2) countries, and transplantation services were available in most countries of the region. Public funding covered the costs of nondialysis chronic kidney disease care in two-thirds of countries, and kidney replacement therapy in nearly all countries. More than half of the countries had dialysis registries; however, national noncommunicable disease strategies were lacking in most countries. The Middle East is a region with high burden of kidney disease and needs cost-effective measures through effective health care funding to be available to improve kidney care in the region. Furthermore, well-designed and sustainable health information systems are needed in the region to address current gaps in kidney care in the region. © 2021 International Society of Nephrolog

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.Comment: 25 pages, 7 figure

The Bayh-Dole Act of 1980 and University–Industry Technology Transfer: A Model for Other OECD Governments?

Recent initiatives by a number of OECD governments suggest considerable interest in emulating the Bayh-Dole Act of 1980, a piece of legislation that is widely credited with stimulating significant growth in university--industry technology transfer and research collaboration in theUS. We examine the effects of Bayh-Dole on university--industry collaboration and technology transfer in the US, emphasizing the lengthy history of both activities prior to 1980 and noting the extent to which these activities are rooted in the incentives created by the unusual scale and structure (by comparison with Western Europe or Japan) of the US higher education system. Efforts at “emulation” of the Bayh-Dole policy elsewhere in the OECD are likely to have modest success at best without greater attention to the underlying structural differences among the higher education systems of these nations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43108/1/10961_2004_Article_5384361.pd

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease