Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

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The role of the dorsal hippocampus in two versions of the touchscreen automated paired associates learning (PAL) task for mice.

RATIONALE: The CANTAB object-location paired-associate learning (PAL) test can detect cognitive deficits in schizophrenia and Alzheimer's disease. A rodent version of touch screen PAL (dPAL) has been developed, but the underlying neural mechanisms are not fully understood. Although there is evidence that inactivation of the hippocampus following training leads to impairments in rats, this has not been tested in mice. Furthermore, it is not known whether acquisition, as opposed to performance, of the rodent version depends on the hippocampus. This is critical as many mouse models may have hippocampal dysfunction prior to the onset of task training. OBJECTIVES: The objectives of this study are to examine the effects of dorsal hippocampal (dHp) dysfunction on both performance and acquisition of mouse dPAL and to determine if hippocampal task sensitivity could be increased using a newly developed context-disambiguated PAL (cdPAL) paradigm. METHODS: In experiment 1, C57Bl/6 mice received post-acquisition dHp infusions of the GABA agonist muscimol. In experiment 2, C57Bl/6 mice received excitotoxic dHp lesions prior to dPAL/cdPAL acquisition. RESULTS: Post-acquisition muscimol dose-dependently impaired dPAL and cdPAL performance. Pre-acquisition dHp lesions had only mild effects on both PAL tasks. Behavioural challenges including addition of objects and degradation of the visual stimuli with noise did not reveal any further impairments. CONCLUSIONS: dPAL and cdPAL performance is hippocampus-dependent in the mouse, but both tasks can be learned in the absence of a functional dHp.CHK received funding from the Korean Health Technology R&D Project, Ministry of Health & Welfare, Republic of Korea (HI11C1183). CJH, LMS and TJB were funded by Medical Research Council/Wellcome Trust grant 089703/Z/09/Z. BAK was funded by a Gates-Cambridge Fellowship. LMS and TJB also received funding from the Innovative Medicine Initiative Joint Undertaking under grant agreement no 115008 of which resources are composed of EFPIA inkind contribution and financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013).This is the final published version. It first appeared from Springer at http://dx.doi.org/10.1007/s00213-015-3949-

Effect of bleaching using sodium hydroxide on pulp derived from Sesbania grandiflora

World demand for paper is increasing. Short rotation pulpwood is needed. Sesbania grandiflora also known as Turi, is a fast growing and straight log species. The scholarly information of Turi as pulpwood are still limited. This paper aims to provide information of sodium hydroxide effect on the paper made from pulp derived from Turi. Sodium hydroxide is a common chemical using as part of full stage chemical bleaching in pulp industrial. Kraft pulp that produced using Turi, was bleached with sodium hydroxide at 3%, 6% and 9% based on pulp weight, respectively. Unbleached pulp was served as blank test. The optical and mechanical properties of handsheet paper made from bleached kraft pulp were evaluated according to TAPPI standard. The brightness and opacity of handsheet made from bleached pulp were improved with increasing the concentration of sodium hydroxide. The mechanical properties of handsheet were improved with using 3% sodium hydroxide and gradually decreased after 3% sodium hydroxide. In conclusion, sodium hydroxide is potential to improve optical properties of Turi pulp and improve the mechanical properties of paper made from Turi pulp at certain level. Excessive usage of sodium hydroxide brings adverse effect to mechanical properties of paper made from Turi pulp

History and Status of ALSEP and the Apollo Lunar Data Project

A suite of automated scientific instruments (the Apollo Lunar Surface Experiment Package, or ALSEP) was installed at each of the landing sites of Apollo 12, 14, 15, 16, and 17 from 1969 to 1972. They operated from deployment until decommissioning on 30 September 1977. These data were continuously transmitted to Earth and saved on the Range Tapes, which were recorded at the Manned Space Flight Network stations. These data were also broken out by experiment and sent to the experiment Principal Investigators on what were called the P.I. Tapes. Starting in April 1973 the Range Tape data were stored in digital format on 7-track magnetic tapes, the ARCSAV Tapes. In February 1976, the handling of the Range Tapes was transferred to UT Galveston. They produced 9-track tapes referred to as the Work Tapes. Following the Apollo program the Range and ARCSAV tapes, which were never archived, were lost. The Work Tapes were archived at the National Space Science Data Center (NSSDC). Some investigators archived their individual experiment data with NSSDC as well, but much of the data had minimal documentation, were not in digital form, or were stored in difficult to translate formats. Data from many experiments were never delivered to the NSSDC. The Lunar Data Project was started to address the problem of both missing and not readily usable data. Our effort has resulted in recovery of some of the ARCSAV tapes, recovery and digitization of a large volume of Apollo scientific and technical documentation, and restoration of many ALSEP and other Apollo data collections. Restoration involves deciphering formats, assembling necessary ancillary data (metadata), and packaging data in digital format to be archived with the Planetary Data System (PDS). Recovery of the data from the ARCSAV tapes involved having the tapes read on special equipment and extracting the individual experiment data out of the integrated data stream. We will report on the history and status of the various recovery efforts

The touchscreen operant platform for assessing executive function in rats and mice.

This protocol details a subset of assays developed within the touchscreen platform to measure various aspects of executive function in rodents. Three main procedures are included: extinction, measuring the rate and extent of curtailing a response that was previously, but is no longer, associated with reward; reversal learning, measuring the rate and extent of switching a response toward a visual stimulus that was previously not, but has become, associated with reward (and away from a visual stimulus that was previously, but is no longer, rewarded); and the 5-choice serial reaction time (5-CSRT) task, gauging the ability to selectively detect and appropriately respond to briefly presented, spatially unpredictable visual stimuli. These protocols were designed to assess both complementary and overlapping constructs including selective and divided visual attention, inhibitory control, flexibility, impulsivity and compulsivity. The procedures comprise part of a wider touchscreen test battery assessing cognition in rodents with high potential for translation to human studies

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

SummaryMicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5′ seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3′ end, with little evidence for 5′ contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding

HIV infection and stroke:current perspectives and future directions

HIV infection can result in stroke via several mechanisms, including opportunistic infection, vasculopathy, cardioembolism, and coagulopathy. However, the occurrence of stroke and HIV infection might often be coincidental. HIV-associated vasculopathy describes various cerebrovascular changes, including stenosis and aneurysm formation, vasculitis, and accelerated atherosclerosis, and might be caused directly or indirectly by HIV infection, although the mechanisms are controversial. HIV and associated infections contribute to chronic inflammation. Combination antiretroviral therapies (cART) are clearly beneficial, but can be atherogenic and could increase stroke risk. cART can prolong life, increasing the size of the ageing population at risk of stroke. Stroke management and prevention should include identification and treatment of the specific cause of stroke and stroke risk factors, and judicious adjustment of the cART regimen. Epidemiological, clinical, biological, and autopsy studies of risk, the pathogenesis of HIV-associated vasculopathy (particularly of arterial endothelial damage), the long-term effects of cART, and ideal stroke treatment in patients with HIV are needed, as are antiretrovirals that are without vascular risk

Characterization of Treponema denticola pyrF encoding orotidine-5′-monophosphate decarboxylase

The Treponema denticola ATCC 35405 genome annotation contains most of the genes for de novo pyrimidine biosynthesis. To initiate characterization of pyrimidine synthesis in Treponema , we focused on TDE2110 (the putative pyrF , encoding orotidine-5′-monophosphate decarboxlyase). Unlike the parent strain, an isogenic pyrF mutant was resistant to 5-fluoroorotic acid. In complex medium, growth of the pyrF mutant was independent of added uracil, indicating activity of a uracil uptake/salvage pathway. Transcription of pyrF was greatly reduced in T. denticola grown in excess uracil, demonstrating that de novo pyrimidine synthesis is regulated and suggesting a feedback mechanism. Treponema denticola PyrF complemented uracil auxotrophy in an Escherichia coli pyrF mutant. This study provides biochemical confirmation of T. denticola genome predictions of de novo and salvage pyrimidine pathways and provides proof of concept that pyrF has potential as a selectable marker in T. denticola .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75261/1/j.1574-6968.2006.00589.x.pd