Imaging the Effector CD8 Synapse.

Here, we describe 4D imaging of effector CD8+ T cells as they conjugate and kill live targets in vitro and analyze the polarization dynamics of intracellular compartments to this cell-cell interface

Opportunities for Public Aquariums to Increase the Sustainability of the Aquatic Animal Trade

The global aquatic pet trade encompasses a wide diversity of freshwater and marine organisms. While relying on a continual supply of healthy, vibrant aquatic animals, few sustainability initiatives exist within this sector. Public aquariums overlap this industry by acquiring many of the same species through the same sources. End users are also similar, as many aquarium visitors are home aquarists. Here we posit that this overlap with the pet trade gives aquariums significant opportunity to increase the sustainability of the trade in aquarium fishes and invertebrates. Improving the sustainability ethos and practices of the aquatic pet trade can carry a conservation benefit in terms of less waste, and protection of intact functioning ecosystems, at the same time as maintaining its economic and educational benefits and impacts. The relationship would also move forward the goal of public aquariums to advance aquatic conservation in a broad sense. For example, many public aquariums in North America have been instrumental in working with the seafood industry to enact positive change toward increased sustainability. The actions include being good consumers themselves, providing technical knowledge, and providing educational and outreach opportunities. These same opportunities exist for public aquariums to partner with the ornamental fish trade, which will serve to improve business, create new, more ethical and more dependable sources of aquatic animals for public aquariums, and perhaps most important, possibly transform the home aquarium industry from a threat, into a positive force for aquatic conservation. Zoo Biol. 32:1-12, 2013. © 2012 Wiley Periodicals, Inc

Mapping targets for small nucleolar RNAs in yeast

Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions

Chandra and Spitzer unveil heavily obscured quasars in the SWIRE/Chandra Survey

Using the large multi-wavelength data set in the chandra/SWIRE Survey (0.6 square degrees in the Lockman Hole), we show evidence for the existence of highly obscured (Compton-thick) AGN, estimate a lower limit to their surface density and characterize their multi-wavelength properties. Two independent selection methods based on the X-ray and infrared spectral properties are presented. The two selected samples contain 1) 5 X-ray sources with hard X-ray spectra and column densities > 10^24 cm-2, and 2) 120 infrared sources with red and AGN-dominated infrared spectral energy distributions (SEDs). We estimate a surface density of at least 25 Compton-thick AGN per square degree detected in the infrared in the chandra/SWIRE field of which ~40% show distinct AGN signatures in their optical/near-infrared SEDs, the remainings being dominated by the host-galaxy emission. Only ~33% of all Compton-thick AGN are detected in the X-rays at our depth (F(0.3-8 keV)>10^-15 erg/cm2/s. We report the discovery of two sources in our sample of Compton-thick AGN, SWIRE_J104409.95+585224.8 (z=2.54) and SWIRE_J104406.30+583954.1 (z=2.43), which are the most luminous Compton-thick AGN at high-z currently known. The properties of these two sources are discussed in detail with an analysis of their spectra, SEDs, luminosities and black-hole masses.Comment: ApJ accepted (to appear in May 2006 issue, vol. 642, of ApJ) Figures 2, 3, and 14 have been degraded due to space consideration

A New Anti-Depressive Strategy for the Elderly: Ablation of FKBP5/FKBP51

The gene FKBP5 codes for FKBP51, a co-chaperone protein of the Hsp90 complex that increases with age. Through its association with Hsp90, FKBP51 regulates the glucocorticoid receptor (GR). Single nucleotide polymorphisms (SNPs) in the FKBP5 gene associate with increased recurrence of depressive episodes, increased susceptibility to post-traumatic stress disorder, bipolar disorder, attempt of suicide, and major depressive disorder in HIV patients. Variation in one of these SNPs correlates with increased levels of FKBP51. FKBP51 is also increased in HIV patients. Moreover, increases in FKBP51 in the amygdala produce an anxiety phenotype in mice. Therefore, we tested the behavioral consequences of FKBP5 deletion in aged mice. Similar to that of naïve animals treated with classical antidepressants FKBP5−/− mice showed antidepressant behavior without affecting cognition and other basic motor functions. Reduced corticosterone levels following stress accompanied these observed effects on depression. Age-dependent anxiety was also modulated by FKBP5 deletion. Therefore, drug discovery efforts focused on depleting FKBP51 levels may yield novel antidepressant therapies

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

<p>Abstract</p> <p>Background</p> <p>Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.</p> <p>Results</p> <p>BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically.</p> <p>Conclusions</p> <p>There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at <url>http://sourceforge.net/projects/brig/</url>.</p

The american pediatric society and society for pediatric research joint statement against racism and social injustice

Although the coronavirus disease 2019 pandemic has served as a flashlight, illuminating and unmasking deep socio-economic and health care divides in our country, the terrible events surrounding the horrific murder of Mr. George Floyd in Minneapolis has spawned even greater outrage. As we all know, Mr. Floyd’s death is not an isolated incident, as there have been a tragic string of such deaths in recent years that further reflect deep issues regarding racism and systemic underlying causes of injustice. Unfortunately, the country’s inability to fully address these systemic foundations of injustice persists

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN