Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq our method enriches for context-specific transcripts over house-keeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d

International Society of Sports Nutrition Position Stand:Probiotics

Position statement: The International Society of Sports Nutrition (ISSN) provides an objective and critical review of the mechanisms and use of probiotic supplementation to optimize the health, performance, and recovery of athletes. Based on the current available literature, the conclusions of the ISSN are as follows: Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host (FAO/WHO). Probiotic administration has been linked to a multitude of health benefits, with gut and immune health being the most researched applications. Despite the existence of shared, core mechanisms for probiotic function, health benefits of probiotics are strain- and dose-dependent. Athletes have varying gut microbiota compositions that appear to reflect the activity level of the host in comparison to sedentary people, with the differences linked primarily to the volume of exercise and amount of protein consumption. Whether differences in gut microbiota composition affect probiotic efficacy is unknown. The main function of the gut is to digest food and absorb nutrients. In athletic populations, certain probiotics strains can increase absorption of key nutrients such as amino acids from protein, and affect the pharmacology and physiological properties of multiple food components. Immune depression in athletes worsens with excessive training load, psychological stress, disturbed sleep, and environmental extremes, all of which can contribute to an increased risk of respiratory tract infections. In certain situations, including exposure to crowds, foreign travel and poor hygiene at home, and training or competition venues, athletes’ exposure to pathogens may be elevated leading to increased rates of infections. Approximately 70% of the immune system is located in the gut and probiotic supplementation has been shown to promote a healthy immune response. In an athletic population, specific probiotic strains can reduce the number of episodes, severity and duration of upper respiratory tract infections. Intense, prolonged exercise, especially in the heat, has been shown to increase gut permeability which potentially can result in systemic toxemia. Specific probiotic strains can improve the integrity of the gut-barrier function in athletes. Administration of selected anti-inflammatory probiotic strains have been linked to improved recovery from muscle-damaging exercise. The minimal effective dose and method of administration (potency per serving, single vs. split dose, delivery form) of a specific probiotic strain depends on validation studies for this particular strain. Products that contain probiotics must include the genus, species, and strain of each live microorganism on its label as well as the total estimated quantity of each probiotic strain at the end of the product’s shelf life, as measured by colony forming units (CFU) or live cells. Preclinical and early human research has shown potential probiotic benefits relevant to an athletic population that include improved body composition and lean body mass, normalizing age-related declines in testosterone levels, reductions in cortisol levels indicating improved responses to a physical or mental stressor, reduction of exercise-induced lactate, and increased neurotransmitter synthesis, cognition and mood. However, these potential benefits require validation in more rigorous human studies and in an athletic population

Physical and Thermal Properties Evaluated of Teflon FEP Retrieved From the Hubble Space Telescope During Three Servicing Missions

Mechanical properties of aluminized Teflon fluorinated ethylene propylene (FEP) thermal control materials on the Hubble Space Telescope (HST) exposed to low Earth orbit for up to 9.7 years have significantly degraded, with extensive cracking occurring on orbit. The NASA Glenn Research Center and the NASA Goddard Space Flight Center have collaborated on analyzing the physical and thermal properties of aluminized FEP (FEP-Al, DuPont) materials retrieved in December 1999 during HST's third servicing mission (SM3A). Comparisons have been made to properties of FEP-Al retrieved during the first and second HST servicing missions, SM1 and SM2, in order to determine degradation processes for FEP on HST

Competence in Endoscopic Ultrasound and Endoscopic Retrograde Cholangiopancreatography, From Training Through Independent Practice.

BACKGROUND & AIMS: It is unclear whether participation in competency-based fellowship programs for endoscopic ultrasound (EUS) and endoscopic retrograde cholangiopancreatography (ERCP) results in high-quality care in independent practice. We measured quality indicator (QI) adherence during the first year of independent practice among physicians who completed endoscopic training with a systematic assessment of competence. METHODS: We performed a prospective multicenter cohort study of invited participants from 62 training programs. In phase 1, 24 advanced endoscopy trainees (AETs), from 20 programs, were assessed using a validated competence assessment tool. We used a comprehensive data collection and reporting system to create learning curves using cumulative sum analysis that were shared with AETs and trainers quarterly. In phase 2, participating AETs entered data into a database pertaining to every EUS and ERCP examination during their first year of independent practice, anchored by key QIs. RESULTS: By the end of training, most AETs had achieved overall technical competence (EUS 91.7%, ERCP 73.9%) and cognitive competence (EUS 91.7%, ERCP 94.1%). In phase 2 of the study, 22 AETs (91.6%) participated and completed a median of 136 EUS examinations per AET and 116 ERCP examinations per AET. Most AETs met the performance thresholds for QIs in EUS (including 94.4% diagnostic rate of adequate samples and 83.8% diagnostic yield of malignancy in pancreatic masses) and ERCP (94.9% overall cannulation rate). CONCLUSIONS: In this prospective multicenter study, we found that although competence cannot be confirmed for all AETs at the end of training, most meet QI thresholds for EUS and ERCP at the end of their first year of independent practice. This finding affirms the effectiveness of training programs. Clinicaltrials.gov ID NCT02509416

Competence in Endoscopic Ultrasound and Endoscopic Retrograde Cholangiopancreatography, From Training Through Independent Practice.

BACKGROUND & AIMS: It is unclear whether participation in competency-based fellowship programs for endoscopic ultrasound (EUS) and endoscopic retrograde cholangiopancreatography (ERCP) results in high-quality care in independent practice. We measured quality indicator (QI) adherence during the first year of independent practice among physicians who completed endoscopic training with a systematic assessment of competence. METHODS: We performed a prospective multicenter cohort study of invited participants from 62 training programs. In phase 1, 24 advanced endoscopy trainees (AETs), from 20 programs, were assessed using a validated competence assessment tool. We used a comprehensive data collection and reporting system to create learning curves using cumulative sum analysis that were shared with AETs and trainers quarterly. In phase 2, participating AETs entered data into a database pertaining to every EUS and ERCP examination during their first year of independent practice, anchored by key QIs. RESULTS: By the end of training, most AETs had achieved overall technical competence (EUS 91.7%, ERCP 73.9%) and cognitive competence (EUS 91.7%, ERCP 94.1%). In phase 2 of the study, 22 AETs (91.6%) participated and completed a median of 136 EUS examinations per AET and 116 ERCP examinations per AET. Most AETs met the performance thresholds for QIs in EUS (including 94.4% diagnostic rate of adequate samples and 83.8% diagnostic yield of malignancy in pancreatic masses) and ERCP (94.9% overall cannulation rate). CONCLUSIONS: In this prospective multicenter study, we found that although competence cannot be confirmed for all AETs at the end of training, most meet QI thresholds for EUS and ERCP at the end of their first year of independent practice. This finding affirms the effectiveness of training programs. Clinicaltrials.gov ID NCT02509416

Highly-efficient Cas9-mediated transcriptional programming

The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease-null Cas9. We demonstrate its utility in activating endogenous coding and noncoding genes, targeting several genes simultaneously and stimulating neuronal differentiation of human induced pluripotent stem cells (iPSCs).National Human Genome Research Institute (U.S.) (Grant P50 HG005550)United States. Dept. of Energy (Grant DE-FG02-02ER63445)Wyss Institute for Biologically Inspired EngineeringNational Science Foundation (U.S.). Graduate Research FellowshipMassachusetts Institute of Technology. Department of Biological EngineeringHarvard Medical School. Department of Genetic

International Society of Sports Nutrition Position Stand: Probiotics.

Position statement: The International Society of Sports Nutrition (ISSN) provides an objective and critical review of the mechanisms and use of probiotic supplementation to optimize the health, performance, and recovery of athletes. Based on the current available literature, the conclusions of the ISSN are as follows: 1)Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host (FAO/WHO).2)Probiotic administration has been linked to a multitude of health benefits, with gut and immune health being the most researched applications.3)Despite the existence of shared, core mechanisms for probiotic function, health benefits of probiotics are strain- and dose-dependent.4)Athletes have varying gut microbiota compositions that appear to reflect the activity level of the host in comparison to sedentary people, with the differences linked primarily to the volume of exercise and amount of protein consumption. Whether differences in gut microbiota composition affect probiotic efficacy is unknown.5)The main function of the gut is to digest food and absorb nutrients. In athletic populations, certain probiotics strains can increase absorption of key nutrients such as amino acids from protein, and affect the pharmacology and physiological properties of multiple food components.6)Immune depression in athletes worsens with excessive training load, psychological stress, disturbed sleep, and environmental extremes, all of which can contribute to an increased risk of respiratory tract infections. In certain situations, including exposure to crowds, foreign travel and poor hygiene at home, and training or competition venues, athletes' exposure to pathogens may be elevated leading to increased rates of infections. Approximately 70% of the immune system is located in the gut and probiotic supplementation has been shown to promote a healthy immune response. In an athletic population, specific probiotic strains can reduce the number of episodes, severity and duration of upper respiratory tract infections.7)Intense, prolonged exercise, especially in the heat, has been shown to increase gut permeability which potentially can result in systemic toxemia. Specific probiotic strains can improve the integrity of the gut-barrier function in athletes.8)Administration of selected anti-inflammatory probiotic strains have been linked to improved recovery from muscle-damaging exercise.9)The minimal effective dose and method of administration (potency per serving, single vs. split dose, delivery form) of a specific probiotic strain depends on validation studies for this particular strain. Products that contain probiotics must include the genus, species, and strain of each live microorganism on its label as well as the total estimated quantity of each probiotic strain at the end of the product's shelf life, as measured by colony forming units (CFU) or live cells.10)Preclinical and early human research has shown potential probiotic benefits relevant to an athletic population that include improved body composition and lean body mass, normalizing age-related declines in testosterone levels, reductions in cortisol levels indicating improved responses to a physical or mental stressor, reduction of exercise-induced lactate, and increased neurotransmitter synthesis, cognition and mood. However, these potential benefits require validation in more rigorous human studies and in an athletic population

Study of multiple roles of the 37/67 kDa laminin receptor in cellular function

The 37/67 kDa laminin receptor (LAMR) is an extracellular receptor, localizes to the nucleus, and plays roles in rRNA processing and ribosome assembly. LAMR is ubiquitously expressed and highly conserved as a member of the S2 ribosomal family, having acquired extracelluar functions through sequence divergence. LAMR is important for cell viability, however it is unclear which of its functions are essential. Additionally, LAMR is overexpressed in many types of cancer, playing roles in tumor cell migration and invasion. Studying LAMR is therefore important from both a cellular functioning and therapeutic standpoint. We found that LAMR is vital for tumor cell proliferation, survival, and protein translation. siRNA mediated reduction in expression of LAMR in HT1080 human fibrosarcoma cells leads to G1 phase cell cycle arrest by altering Cyclin A2/B1, CDK1/2, Survivin, and p21 expression levels. HT1080 cells treated with siRNA become morphologically distinct and lose mitochondrial membrane potential, developing a sub-G1/apoptoic population. Further, reduction in LAMR expression leads to a dramatic decrease in newly synthesized proteins due to reduction in 40S subunits and 80S monosomes, and an increase in unassociated 60S ribosomal subunits. Ultimately, reduction in LAMR expression inhibits HT1080 tumor development in vivo. To clarify which functions of LAMR are responsible for maintaining viability, we developed a silent mutant LAMR construct resistant to siRNA to rescue the phenotypic effects of knocking down endogenous LAMR. Additionally, we generated a C-terminal truncated silent mutant LAMR construct structurally homologous to the A. fulgidus S2 ribosomal protein and missing the C-terminal 75 amino acids of LAMR, which displays more sequence divergence. We found HT1080 cells stably expressing either silent mutant LAMR construct still undergo arrest in the G1 phase of the cell cycle when treated with siRNA. However, expression of full-length silent mutant LAMR rescues cell viability while expression of the C-terminal truncated LAMR does not. Interestingly, we also found that both silent mutant constructs restore protein translation and localize to the nucleus. Our findings indicate that the ability of LAMR to regulate viability is associated with its C-terminal 75 residues. Further, this function is distinct from its role in cell proliferation, independent of its ribosomal functions, and may be regulated by a non-nuclear localization

Impact of probiotic Veillonella atypica FB0054 supplementation on anaerobic capacity and lactate

Summary: Seven healthy, physically active men (n = 3) and women (n = 4) (30.7 ± 7.5 years, 172.7 ± 8.7 cm, 70.4 ± 11.6 kg, 23.6 ± 4.1 kg/m2, 49.2 ± 8.4 mL/kg/min) supplemented for 14 days with a placebo (PLA) or 1 × 1010 CFU doses of the probiotic Veillonella atypica FB0054 (FitBiomics, New York, NY). Participants had safety panels, hemodynamics, lactate, and anaerobic capacity assessed. Stool samples were collected to evaluate for metagenomic and metabolomic changes. Exhaustion times were not different between groups, whereas anaerobic capacity tended to shorten with PLA (61.14 ± 72.04 s; 95% CI: −5.49, 127.77 s, p = 0.066) with no change with VA (13.29 ± 100.13 s, 95% CI: −79.32, 105.89 s, p = 0.738). No changes in lactate, hemodynamics, or bacterial community changes were observed, whereas 14 metabolites exhibited differential expression patterns with VA supplementation. In conclusion, VA maintained exercise performance that tended to decline in PLA. Supplementation was well tolerated with no changes in safety markers or reported adverse events

Patching vs atropine to treat amblyopia in children aged 7 to 12 years: a randomized trial

To compare patching with atropine eyedrops in the treatment of moderate amblyopia (visual acuity, 20/40-20/100) in children aged 7 to 12 years. In a randomized, multicenter clinical trial, 193 children with amblyopia were assigned to receive weekend atropine or patching of the sound eye 2 hours per day. Main Outcome Measure Masked assessment of visual acuity in the amblyopic eye using the electronic Early Treatment Diabetic Retinopathy Study testing protocol at 17 weeks. At 17 weeks, visual acuity had improved from baseline by an average of 7.6 letters in the atropine group and 8.6 letters in the patching group. The mean difference between groups (patching - atropine) adjusted for baseline acuity was 1.2 letters (ends of complementary 1-sided 95% confidence intervals for noninferiority, -0.7, 3.1 letters). This difference met the prespecified definition for equivalence (confidence interval <5 letters). Visual acuity in the amblyopic eye was 20/25 or better in 15 participants in the atropine group (17%) and 20 in the patching group (24%; difference, 7%; 95% confidence interval, -3% to 17%). Treatment with atropine or patching led to similar degrees of improvement among 7- to 12-year-olds with moderate amblyopia. About 1 in 5 achieved visual acuity of 20/25 or better in the amblyopic eye. Atropine and patching achieve similar results among older children with unilateral amblyopia. (clinicaltrials.gov) Identifier: NCT00315328