Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes

Kidney: Papillary adenoma

Review on Renal papillary adenoma, with data on clinics, and the genes involved

Balloon Atrial Septostomy as Initial Therapy in Pediatric Pulmonary Hypertension

Balloon atrial septostomy is a palliative procedure currently used to bridge medically refractory pulmonary hypertension patients to lung transplantation. In the current report, we present balloon atrial septostomy as an initial therapy for high-risk pediatric pulmonary hypertension patients at our institution. Nineteen patients with median age of 4.3 years (range 0.1-14.3 years) underwent balloon atrial septostomy during initial admission for pulmonary hypertension. There were no procedural complications or deaths within 24 h of balloon atrial septostomy. Patients were followed for a median of 2.6 years (interquartile range 1.0-4.8 years). Three (16%) patients died, 3 (16%) underwent lung transplantation, and 1 (5%) underwent reverse Potts shunt. Transplant-free survival at 30 days, 1 year, and 3 years was 84%, 76%, and 67% respectively. This single-center experience suggests early-BAS in addition to pharmacotherapy is safe and warrants consideration in high-risk pediatric pulmonary hypertension patients

Kidney: Metanephric adenoma

Review on Kidney metanephric adenoma a, with data on clinics, and the genes involved

Internship Experiences Contribute to Confident Career Decision Making for Doctoral Students in the Life Sciences.

The Graduate Student Internships for Career Exploration (GSICE) program at the University of California, San Francisco (UCSF), offers structured training and hands-on experience through internships for a broad range of PhD-level careers. The GSICE program model was successfully replicated at the University of California, Davis (UC Davis). Here, we present outcome data for a total of 217 PhD students participating in the UCSF and UC Davis programs from 2010 to 2015 and 2014 to 2015, respectively. The internship programs at the two sites demonstrated comparable participation, internship completion rates, and overall outcomes. Using survey, focus group, and individual interview data, we find that the programs provide students with career development skills, while increasing students' confidence in career exploration and decision making. Internships, in particular, were perceived by students to increase their ability to discern a career area of choice and to increase confidence in pursuing that career. We present data showing that program participation does not change median time to degree and may help some trainees avoid "default postdocs." Our findings suggest important strategies for institutions developing internship programs for PhD students, namely: including a structured training component, allowing postgraduation internships, and providing a central organization point for internship programs

River chloride trends in snow-affected urban watersheds: increasing concentrations outpace urban growth rate and are common among all seasons

AbstractChloride concentrations in northern U.S. included in this study have increased substantially over time with average concentrations approximately doubling from 1990 to 2011, outpacing the rate of urbanization in the northern U.S. Historical data were examined for 30 monitoring sites on 19 streams that had chloride concentration and flow records of 18 to 49years. Chloride concentrations in most studied streams increased in all seasons (13 of 19 in all seasons; 16 of 19 during winter); maximum concentrations occurred during winter. Increasing concentrations during non-deicing periods suggest that chloride was stored in hydrologic reservoirs, such as the shallow groundwater system, during the winter and slowly released in baseflow throughout the year. Streamflow dependency was also observed with chloride concentrations increasing as streamflow decreased, a result of dilution during rainfall- and snowmelt-induced high-flow periods. The influence of chloride on aquatic life increased with time; 29% of sites studied exceeded the concentration for the USEPA chronic water quality criteria of 230mg/L by an average of more than 100 individual days per year during 2006–2011. The rapid rate of chloride concentration increase in these streams is likely due to a combination of possible increased road salt application rates, increased baseline concentrations, and greater snowfall in the Midwestern U.S. during the latter portion of the study period

DNA-Based Authentication of Botanicals and Plant-Derived Dietary Supplements: Where Have We Been and Where Are We Going?

Herbal medicines and botanicals have long been used as sole or additional medical aids worldwide. Currently, billions of dollars are spent on botanicals and related products, but minimal regulation exists regarding their purity, integrity, and efficacy. Cases of adulteration and contamination have led to severe illness and even death in some cases. Identifying the plant material in botanicals and phytomedicines using organoleptic means or through microscopic observation of plant parts is not trivial, and plants are often misidentified. Recently, DNA-based methods have been applied to these products because DNA is not changed by growth conditions unlike the chemical constituents of many active pharmaceutical agents. In recent years, DNA barcoding methods, which are used to identify species diversity in the Tree of Life, have been also applied to botanicals and plant-derived dietary supplements. In this review, we recount the history of DNA-based methods for identification of botanicals and discuss some of the difficulties in defining a specific bar code or codes to use. In addition, we describe how next generation sequencing technologies have enabled new techniques that can be applied to identifying these products with greater authority and resolution. Lastly, we present case histories where dietary supplements, decoctions, and other products have been shown to contain materials other than the main ingredient stipulated on the label. We conclude that there is a fundamental need for greater quality control in this industry, which if not self-imposed, that may result from legislation

Left-ventricular outflow tract acceleration time is associated with symptoms in patients with obstructive hypertrophic cardiomyopathy

AIMS: Not all obstructive hypertrophic cardiomyopathy (HCM) patients are symptomatic. The relation between obstructive HCM and symptoms is not well understood. The hypothesis of this study is that left-ventricular outflow tract (LVOT) acceleration time (AT) is associated with symptoms. METHODS: We included 187 patients (61% men, mean age 55 ± 14 years) with obstructive HCM, defined as a maximal wall thickness ≥ 15 mm and a resting or provoked LVOT peak gradient ≥ 30 mmHg. Peak velocity (PV), left-ventricular (LV) ejection time (ET), and AT (the time between LVOT flow onset and the moment of PV) were measured on continuous-wave (CW) Doppler tracings. Logistic and Cox proportional hazard regression analyses were used to evaluate the relation between symptoms [New York Heart Association (NYHA) class ≥ II] and echocardiographic measurements, including AT. Reproducibility was assessed using the intraclass correlation coefficient (ICC). RESULTS: Symptomatic patients were more often female and had higher mean AT values. Logistic regression demonstrated a significant association between AT and symptomatic status (odds ratio 1.31 per 10 ms, p < 0.01) after adjustment for sex, negative inotropes, PV, LVOT diameter, and diastolic dysfunction. AT was independently associated with symptoms and septal reduction during follow-up (hazard ratio 1.09 per 10 ms, p < 0.05). The ICC was 0.98 with a mean difference of 0.28 ± 8.4 ms. CONCLUSION: In obstructive HCM patients, increased AT is significantly related to symptoms after adjustment for sex, negative inotropes, PV, LVOT diameter, and diastolic dysfunction, and is associated with the symptomatic status during follow-up. AT represents an easily measured echocardiographic variable with excellent inter-reader reproducibility. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40477-020-00513-3) contains supplementary material, which is available to authorized users