Evaluating biogenesis of 5’-tailed mirtrons

MicroRNAs are 22 nucleotide, non-coding RNAs that serve as substrates for Argonaute proteins to induce RNA interference pathways. Intron-derived miRNA precursors called “mirtrons” have been identified and classified primarily through deep sequencing methods. Unlike most miRNAs, mirtrons are derived from splicing events and also exhibit high levels of post-transcriptional nucleotide addition to hairpin precursors. Most relevant among these modifications is 3’ uridylation as it inhibits mirtron biogenesis in multiple model systems. Mirtrons may also possess additional nucleotides adjacent to the pre-miRNA hairpin at the 3’ and/or 5’ ends. These nucleotide “tails” are removed prior to Dicer cleaving the hairpin. In 2010, Flynt et al. reported that tail trimming activity in the highly conserved 3’-tailed mirtron dme-miR-1017 was performed by the RNA exosome. The insertion of a tract of guanines within the tail would prevent trimming if the activity is performed by an exoribonuclease. To determine if tail removal in 5’-tailed mirtrons is also exosome-mediated, three mutant constructs including a 12 G insert, 20-bp splice site insert and a splice site mutant (negative control) were derived from hsa-miR-5010 and used for comparing target repression levels and base modification. We employed cell culture, transfection, luciferase assay and sequence analysis to determine the effect of differential tail elements on miRNA processing and activity. Our findings confirm selective uridylation at the 3’ end for all miR-5010 variants. The Poly G mutant had greater activity and stability compared to both the wild-type and the splice site mutant. These data imply that 5’-tailed mirtron tail removal is mediated by an endoribonuclease unlike the 3’-tailed variants

A Sense of Duty: Retiring the Special Relationship Rule and Holding Gun Manufacturers Liable for Negligently Distributing Guns

In response to recent litigation brought against the gun industry on behalf of individuals and municipalities victimized as a result of the negligent marketing, design, and distribution of guns, the gun industry has argued that they cannot be held responsible for the victims\u27 injuries because they have no special relationship with the victims. Without a special relationship, gun manufacturers claim to have no duty whatsoever to design, market, or distribute guns in a reasonable fashion. This article examines the fallacies inherent in the gun industry\u27s special relationship argument and discusses the factual, legal and policy grounds that support holding the gun industry responsible for its role in facilitating the misuse of guns

Insect Floral Visitors of Red Maple and Tree-of-Heaven at Potential Risk of Neonicotinoid Residue Exposure from Spotted Lanternfly Control

To manage spotted lanternfly (Lycorma delicatula (White)), an invasive planthopper recently introduced to the United States, governmental agencies, homeowners, and landscape professionals may treat its host plants with systemic neonicotinoid insecticides. Neonicotinoids can be harmful to non-target insect floral visitors collecting pollen or nectar. The insect floral visitors of red maple (Acer rubrum L.) or tree-of-heaven (Ailanthus altissima (Mill.), which are two of the preferred hosts of L. delicatula in Pennsylvania, are often targeted with neonicotinoid applications for control of this pest. To identify the floral visitors of these tree species, we conducted observations and collections of insects foraging on the flowers of these trees in Pennsylvania during the annual bloom period. In southeastern Pennsylvania, the margined leatherwing beetle (Chauliognathus marginatus (F.)). was the most dominant visitor of tree-of-heaven flowers, followed in abundance by bees, particularly Lasioglossum and Bombus spp., and flies. In central and southeastern Pennsylvania, bees were the most dominant group to visit red maple flowers, particularly Apis mellifera (L.), Andrena spp. and Osmia spp., followed by flies. These results contribute to our knowledge of the pool of bioindicator insects that may be at risk from exposure to neonicotinoid residues in flowers of trees treated for L. delicatula management

Tracing/training rebellion - object work in Meyerhold's biomechanics

[First paragraph] Lying in the Russian State Archive of Literature and Arts in Moscow (RGALI) is a nine-page document entitled Programme of Biomechanics, Meyerhold Workshop (1922). Though modest in size, it is an unashamedly ambitious programme, which sought to redefine acting in a post-revolutionary context and to place performer training in Russia on a par with science. ‘The task of the biomechanical laboratory is to work out through experimentation a biomechanical system of acting and of actor’s training’ (Hoover 1974: 314), the document claims, setting out a dedicated model of Practice as Research, seventy years before the term became common place in the UK

Time-Sliced Quantum Circuit Partitioning for Modular Architectures

Current quantum computer designs will not scale. To scale beyond small prototypes, quantum architectures will likely adopt a modular approach with clusters of tightly connected quantum bits and sparser connections between clusters. We exploit this clustering and the statically-known control flow of quantum programs to create tractable partitioning heuristics which map quantum circuits to modular physical machines one time slice at a time. Specifically, we create optimized mappings for each time slice, accounting for the cost to move data from the previous time slice and using a tunable lookahead scheme to reduce the cost to move to future time slices. We compare our approach to a traditional statically-mapped, owner-computes model. Our results show strict improvement over the static mapping baseline. We reduce the non-local communication overhead by 89.8\% in the best case and by 60.9\% on average. Our techniques, unlike many exact solver methods, are computationally tractable.Comment: Appears in CF'20: ACM International Conference on Computing Frontier

Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-locked lakes of Schirmacher Oasis and the Perennially Ice-covered Lake Untersee in East Antarctica

Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions

Study of the Microbial Diversity of a Newly Discovered East Antarctic Freshwater Lake, L27C, and of a Perennially Ice-Covered Lake Untersee

The microbial communities that reside within freshwater lakes of Schirmacher and Untersee Oases in East Antarctica must cope with extreme conditions that may include cold temperature, annual freeze-thaw cycles, exposure to UV radiation, especially during the austral summer months, low light beneath thick ice-cover, followed by seasonal darkness. The objective of this study was to assess the microbial biodiversity and distribution from samples taken from two freshwater lakes (L27C and Lake Untersee) that were collected during the Tawani 2008 International Antarctic Expedition that conducted research in this region of Antarctica. L27C is a small, previously unreported lake residing 2 km WNW of Maitri Station at Schirmacher Oasis. Biodiversity and distribution of microorganisms within the lake were studied using both culture-independent and culture-dependent methodologies based upon the analysis of eubacterial 16S rRNA gene sequences. Lake Untersee, a perennially ice-covered, ultra-oligotrophic, lake in the Otto-von-Gruber-Gebirge (Gruber Mountains) of central Dronning Maud Land was also sampled and the microbial diversity was analyzed by eubacterial 16S rRNA gene sequences derived from pure cultures. Direct culturing of water samples from each lake on separate R2A growth medium exhibited a variety of microorganisms including: Janthinobacterium, Hymenobacter, Sphingamonas, Subtercola, Deinococcus, Arthrobacter, Flavobacterium, Polaromonas, Rhodoferax and Duganella. The evaluation of samples from L27C through culture-independent methodology identified a rich microbial diversity consisting of six different phyla of bacteria. The culture-independent analysis also displayed the majority of bacteria (56%) belonged to the Class gamma-proteobacteria within the phylum Proteobacteria. Within the Class gamma-proteobacteria, Acinetobacter dominated (48%) the total microbial load. Overall, L27C exhibited 7 different phyla of bacteria and 20 different genera. Statistical analysis (Shannon-Weaver Diversity Index and Simpson Diversity Index) of the biodiversity of L27C displayed a moderately rich and diverse community. Investigations of the biodiversity and distribution of microorganisms in these lakes will help further our understanding of how the physical environment impact the structure and function within these microbially dominated ecosystems

A global soil spectral calibration library and estimation service

There is growing global interest in the potential for soil reflectance spectroscopy to fill an urgent need for more data on soil properties for improved decision-making on soil security at local to global scales. This is driven by the capability of soil spectroscopy to estimate a wide range of soil properties from a rapid, inexpensive, and highly reproducible measurement using only light. However, several obstacles are preventing wider adoption of soil spectroscopy. The biggest obstacles are the large variation in the soil analytical methods and operating procedures used in different laboratories, poor reproducibility of analyses within and amongst laboratories and a lack of soil physical archives. In addition, adoption is hindered by the expense and complexity of building soil spectral libraries and calibration models. The Global Soil Spectral Calibration Library and Estimation Service is proposed to overcome these obstacles by providing a freely available estimation service based on an open, high quality and diverse spectral calibration library and the extensive soil archives of the Kellogg Soil Survey Laboratory (KSSL) of the Natural Resources Conservation Service of the United States Department of Agriculture (USDA). The initiative is supported by the Global Soil Laboratory Network (GLOSOLAN) of the Global Soil Partnership and the Soil Spectroscopy for Global Good network, which provide additional support through dissemination of standards, capacity development and research. This service is a global public good which stands to benefit soil assessments globally, but especially developing countries where soil data and resources for conventional soil analyses are most limited

A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts.

Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods. To address this hurdle, we developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, we demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity. Previous studies have suggested that pancreatic ductal adenocarcinoma (PDAC) gene expression signatures vary significantly under in vitro versus in vivo and in vivo subcutaneous versus orthotopic conditions. By using our improved mH-based method, we were able to preserve established expression patterns of KRas-dependency genes within these three unique microenvironments. Finally, expression analysis of novel biomarkers in KRas mutant PDAC samples revealed that PEAK1 decreases and MST1R increases by over 100-fold in orthotopic versus subcutaneous microenvironments. Interestingly, however, only PEAK1 levels remain elevated in orthotopically grown KRas wild-type PDAC cells. These results demonstrate the critical nature of the orthotopic tumor microenvironment when evaluating the clinical relevance of new biomarkers in cells or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to enhance and expand future FFPE-RNA-NGS cancer biomarker studies

Association Between Pregnancy at Enrollment into HIV Care and Loss to Care Among Women in the Democratic Republic of Congo, 2006-2013

BACKGROUND: Loss to care is high among asymptomatic HIV-infected women initiated on antiretroviral therapy (ART) during pregnancy or in the postpartum period. However, whether pregnancy itself plays a role in the high loss to care rate is uncertain. We compared loss to care over seven years between pregnant and non-pregnant women at enrollment into HIV care in the Democratic Republic of Congo (DRC). METHODS: We conducted a retrospective analysis of all ART-naive women aged 15-45 initiating HIV care at two large clinics in Kinshasa, DRC, from 2007-2013. Pregnancy status was recorded at care enrollment. Patients were classified as having no follow-up if they did not return to care after the initial enrollment visit. Among those with at least one follow-up visit after enrollment, we classified patients as lost to care if more than 365 days had passed since their last clinic visit. We used logistic regression to model the association between pregnancy status and no follow-up, and Cox proportional hazards regression to model the association between pregnancy status and time to loss to care. RESULTS: Of 2175 women included in the analysis, 1497 (68.8%) were pregnant at enrollment. Compared to non-pregnant women, pregnant women were less likely to be over 35 years of age (19.1% vs. 31.9%,