A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods.

Background3' RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and the 3' method is needed to determine their relative merits. To this end, we used two commercially available library preparation kits, the KAPA Stranded mRNA-Seq kit (traditional method) and the Lexogen QuantSeq 3' mRNA-Seq kit (3' method), to prepare libraries from mouse liver RNA. We then sequenced and analyzed the libraries to determine the advantages and disadvantages of these two approaches.ResultsWe found that the traditional whole transcript method and the 3' RNA-Seq method had similar levels of reproducibility. As expected, the whole transcript method assigned more reads to longer transcripts, while the 3' method assigned roughly equal numbers of reads to transcripts regardless of their lengths. We found that the 3' RNA-Seq method detected more short transcripts than the whole transcript method. With regard to differential expression analysis, we found that the whole transcript method detected more differentially expressed genes, regardless of the level of sequencing depth.ConclusionsThe 3' RNA-Seq method was better able to detect short transcripts, while the whole transcript RNA-Seq was able to detect more differentially expressed genes. Thus, both approaches have relative advantages and should be selected based on the goals of the experiment

Algal Blooms in Arkansas Streams, Ponds, and Lakes

Did you know that algae are a natural part of ponds, lakes, streams, and rivers? These organisms grow in the water (plankton) and on rocks, plants, and other surfaces (periphyton) and sometimes periphyton slough off into the water (seston). Most of the time these algae are hardly noticeable in waterbodies; however, sometimes they can form very noticeable algal blooms

Granular Packings: Nonlinear elasticity, sound propagation and collective relaxation dynamics

Experiments on isotropic compression of a granular assembly of spheres show that the shear and bulk moduli vary with the confining pressure faster than the 1/3 power law predicted by Hertz-Mindlin effective medium theories (EMT) of contact elasticity. Moreover, the ratio between the moduli is found to be larger than the prediction of the elastic theory by a constant value. The understanding of these discrepancies has been a longstanding question in the field of granular matter. Here we perform a test of the applicability of elasticity theory to granular materials. We perform sound propagation experiments, numerical simulations and theoretical studies to understand the elastic response of a deforming granular assembly of soft spheres under isotropic loading. Our results for the behavior of the elastic moduli of the system agree very well with experiments. We show that the elasticity partially describes the experimental and numerical results for a system under compressional loads. However, it drastically fails for systems under shear perturbations, particularly for packings without tangential forces and friction. Our work indicates that a correct treatment should include not only the purely elastic response but also collective relaxation mechanisms related to structural disorder and nonaffine motion of grains.Comment: 21 pages, 13 figure

The impact of abnormal glucose tolerance and obesity on fetal growth

Factors linked with insulin resistance were examined for their association with large-for-gestational-age (LGA) infant birth weight and gestational diabetes. Study Design. Data came from a longitudinal cohort study of 2,305 subjects without overt diabetes, analyzed using multinomial logistic and linear regression. Results. High maternal BMI (OR = 1.53 (1.11, 2.12)), height (1.98 (1.62, 2.42)), antidepressant use (1.71 (1.20, 2.44)), pregnancy weight-gain exceeding 40 pounds (1.79 (1.25, 2.57)), and high blood sugar (2.68, (1.53, 5.27)) were all positively associated with LGA birth. Strikingly, the difference in risk from diagnosed and treated gestational diabetes compared to women with a single abnormal glucose tolerance test (but no diagnosis of gestational diabetes) was significant (OR = 0.65, p = 0.12 versus OR = 2.84, p \u3c 0.01). When weight/length ratio was used instead, different factors were found to be significant. BMI and pregnancy weight-gain were found to influence the development of gestational diabetes, through an additive interaction. Conclusions. High prepregnancy BM, height, antidepressant use, pregnancy weight-gain exceeding 40 pounds, and high blood sugar were associated with LGA birth, but not necessarily infant weight/length ratio. An additive interaction between BMI and pregnancy weight-gain influenced gestational diabetes development

Coming Home: Health Status and Homelessness Risk of Older Pre-release Prisoners

Older adults comprise an increasing proportion of the prison and homeless populations. While older age is associated with adverse post-release health events and incarceration is a risk factor for homelessness, the health status and homelessness risk of older pre-release prisoners are unknown. Moreover, most post-release services are geared towards veterans; it is unknown whether the needs of non-veterans differ from those of veterans. To assess health status and risk of homelessness of older pre-release prisoners, and to compare veterans with non-veterans. Cross-sectional study of 360 prisoners (≥55 years of age) within 2 years of release from prison using data from the 2004 Survey of Inmates in State and Federal Correctional Facilities. Veteran status, health status (based on self-report), and risk of homelessness (homelessness before arrest). Mean age was 61 years; 93.8% were men and 56.5% were white. Nearly 40% were veterans, of whom 77.2% reported likely VA service eligibility. Veterans were more likely to be white and to have obtained a high school diploma or GED. Overall, 79.1% reported a medical condition and 13.6% reported a serious mental illness. There was little difference in health status between veterans and non-veterans. Although 1 in 12 prisoners reported a risk factor for homelessness, the risk factors did not differ according to veteran status. Older pre-release prisoners had a high burden of medical and mental illness and were at risk for post-release homelessness regardless of veteran status. Reentry programs linking pre-release older prisoners to medical and psychiatric services and to homelessness prevention programs are needed for both veterans and non-veterans

Professional Development for Early Career DBER Scholars through In-Person and Virtual Career Panel Workshops

In discipline-based education research (DBER), early career scholars, such as graduate students and postdoctoral researchers, observe a slew of possible career pathways. Yet, there is a lack of opportunities to learn about such pathways, particularly when transitioning from traditional science, technology, engineering, or math (STEM) disciplinary training into a DBER position. Thus, the DBER Scholars-in-Training Professional Development subcommittee was created within the Society for the Advancement of Biology Education Research (SABER) community to develop a collection of workshops that would serve the greatest professional development needs of early career scholars entering DBER. Through a series of surveys disseminated over multiple years, early career scholars expressed interest in better navigating their career options, which led to the development of the career panel workshop, held during the 2019 and 2020 SABER Annual National Conferences. In this report, we explore the development, implementation, and results of two career panel workshops and compare and contrast the 2019 in-person workshop with the 2020 virtual workshop. We also offer our insights on the value of the career workshop, discuss the next steps, and explore valuable resources for those planning on organizing similar events

Brain Cell-Type Shifts in Alzheimer’s Disease, Autism, and Schizophrenia Interrogated Using Methylomics and Genetics

Few neuropsychiatric disorders have replicable biomarkers, prompting high-resolution and large-scale molecular studies. However, we still lack consensus on a more foundational question: whether quantitative shifts in cell types-the functional unit of life-contribute to neuropsychiatric disorders. Leveraging advances in human brain single-cell methylomics, we deconvolve seven major cell types using bulk DNA methylation profiling across 1270 postmortem brains, including from individuals diagnosed with Alzheimer\u27s disease, schizophrenia, and autism. We observe and replicate cell-type compositional shifts for Alzheimer\u27s disease (endothelial cell loss), autism (increased microglia), and schizophrenia (decreased oligodendrocytes), and find age- and sex-related changes. Multiple layers of evidence indicate that endothelial cell loss contributes to Alzheimer\u27s disease, with comparable effect size to APOE genotype among older people. Genome-wide association identified five genetic loci related to cell-type composition, involving plausible genes for the neurovascular unit (P2RX5 and TRPV3) and excitatory neurons (DPY30 and MEMO1). These results implicate specific cell-type shifts in the pathophysiology of neuropsychiatric disorders