Peptides encoded by short ORFs control development and define a new eukaryotic gene family

Despite recent advances in developmental biology and in genomics, key questions remain regarding the organisation of cells into embryos. One possibility is that novel types of genes might await discovery and could provide some of the answers. Genome annotation depends strongly on comparison with previously known gene sequences, and so genes having previously uncharacterised structure and function can be missed. Here we present the characterisation of tarsal-less, a new such type of gene. Tarsal-less has two unusual features: first, it contains more than one coding unit, a structure more similar to some bacterial genes. Second, it codes for small peptides rather than proteins, and in fact these peptides represent the smallest gene products known to date. Functional analysis of this gene in the fruitfly Drosophila shows that it has important functions throughout development, including tissue morphogenesis and pattern formation. We identify genes similar to tarsal-less in other species, and thus define a tarsal-less-related gene family. We expect that a combination of bioinformatic and functional methods, such as the ones we use in this study, will identify and characterize more genes of this type. Potentially, thousands of such new genes may exist

2016-2017 Mostly Music: Robert Schumann

https://spiral.lynn.edu/conservatory_mostlymusic/1028/thumbnail.jp

Shelf-derived iron inputs drive biological productivity in the southern Drake Passage

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 23 (2009): GB4014, doi:10.1029/2008GB003406.In the Southern Ocean near the Antarctic Peninsula, Antarctic Circumpolar Current (ACC) fronts interact with shelf waters facilitating lateral transport of shelf-derived components such as iron into high-nutrient offshore regions. To trace these shelf-derived components and estimate lateral mixing rates of shelf water, we used naturally occurring radium isotopes. Short-lived radium isotopes were used to quantify the rates of shelf water entrainment while Fe/228Ra ratios were used to calculate the Fe flux. In the summer of 2006 we found rapid mixing and significant lateral iron export, namely, a dissolved iron flux of 1.1 × 105 mol d−1 and total acid leachable iron flux of 1.1 × 106 mol d−1 all of which is transported in the mixed layer from the shelf region offshore. This dissolved iron flux is significant, especially considering that the bloom observed in the offshore region (0.5–2 mg chl a m−3) had an iron demand of 1.1 to 4 × 105 mol Fe. Net vertical export fluxes of particulate Fe derived from 234Th/238U disequilibrium and Fe/234Th ratios accounted for only about 25% of the dissolved iron flux. On the other hand, vertical upward mixing of iron rich deeper waters provided only 7% of the lateral dissolved iron flux. We found that similarly to other studies in iron-fertilized regions of the Southern Ocean, lateral fluxes overwhelm vertical inputs and vertical export from the water column and support significant phytoplankton blooms in the offshore regions of the Drake Passage.This work was funded by the National Science Foundation (ANT-0443869 to M.A.C.)

Analysis and Functional Annotation of Expressed Sequence Tags from the Asian Longhorned Beetle, Anoplophora glabripennis

The Asian longhorned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), is one of the most economically and ecologically devastating forest insects to invade North America in recent years. Despite its substantial impact, limited effort has been expended to define the genetic and molecular make-up of this species. Considering the significant role played by late-stadia larvae in host tree decimation, a small-scale EST sequencing project was done using a cDNA library constructed from 5th -instar A. glabripennis. The resultant dataset consisted of 599 high quality ESTs that, upon assembly, yielded 381 potentially unique transcripts. Each of these transcripts was catalogued as to putative molecular function, biological process, and associated cellular component according to the Gene Ontology classification system. Using this annotated dataset, a subset of assembled sequences was identified that are putatively associated with A. glabnpennis development and metamorphosis. This work will contribute to understanding of the diverse molecular mechanisms that underlie coleopteran morphogenesis and enable the future development of novel control strategies for management of this insect pest

Isolation of Primary Human Hepatocytes from Normal and Diseased Liver Tissue: A One Hundred Liver Experience

Successful and consistent isolation of primary human hepatocytes remains a challenge for both cell-based therapeutics/transplantation and laboratory research. Several centres around the world have extensive experience in the isolation of human hepatocytes from non-diseased livers obtained from donor liver surplus to surgical requirement or at hepatic resection for tumours. These livers are an important but limited source of cells for therapy or research. The capacity to isolate cells from diseased liver tissue removed at transplantation would substantially increase availability of cells for research. However no studies comparing the outcome of human hepatocytes isolation from diseased and non-diseased livers presently exist. Here we report our experience isolating human hepatocytes from organ donors, non-diseased resected liver and cirrhotic tissue. We report the cell yields and functional qualities of cells isolated from the different types of liver and demonstrate that a single rigorous protocol allows the routine harvest of good quality primary hepatocytes from the most commonly accessible human liver tissue samples

The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector.

The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies

Noise Characterization and Filtering in the MicroBooNE Liquid Argon TPC

The low-noise operation of readout electronics in a liquid argon time projection chamber (LArTPC) is critical to properly extract the distribution of ionization charge deposited on the wire planes of the TPC, especially for the induction planes. This paper describes the characteristics and mitigation of the observed noise in the MicroBooNE detector. The MicroBooNE's single-phase LArTPC comprises two induction planes and one collection sense wire plane with a total of 8256 wires. Current induced on each TPC wire is amplified and shaped by custom low-power, low-noise ASICs immersed in the liquid argon. The digitization of the signal waveform occurs outside the cryostat. Using data from the first year of MicroBooNE operations, several excess noise sources in the TPC were identified and mitigated. The residual equivalent noise charge (ENC) after noise filtering varies with wire length and is found to be below 400 electrons for the longest wires (4.7 m). The response is consistent with the cold electronics design expectations and is found to be stable with time and uniform over the functioning channels. This noise level is significantly lower than previous experiments utilizing warm front-end electronics.Comment: 36 pages, 20 figure

Convolutional Neural Networks Applied to Neutrino Events in a Liquid Argon Time Projection Chamber

We present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identification or event detection on simulated neutrino interactions. We also address technical issues that arise when applying this technique to data from a large LArTPC at or near ground level