Rapid Data Entry: Supporting high-throughput digitisation workflows in EMu

<p><strong>Presentation given at the Taxonomic Data Working Group (TDWG) meeting, 28 October 2014 - Jönköping, Sweden</strong></p> <p><strong><br></strong></p> <p><strong>Abstract</strong>: Over the next five years the Natural History Museum is embarking on a programme to digitise significant numbers of specimens with the aim to make the resulting data freely available online in the museum's Data Portal. In order to support this a new highly customisable web-based platform, Rapid Data Entry (RDE), has been developed for the museum’s content management system, EMu.</p> <p>RDE is composed of three parts: 1) a project creation and administration interface that allows data managers to create customisable web applications for specific digitisation projects that directly reference back-end fields in EMu; 2) forms for rapid data entry and editing that can be used on both desktop and mobile clients; 3) editors that support the normalisation of data.</p> <p>The general advantages and disadvantages of an alternative web interface to a traditional desktop client are discussed along with potential new workflows such as: specimen relocation via barcodes, condition checking, collections audit and other targeted data capture activities.</p

Tissue Specific Expression of Cre in Rat Tyrosine Hydroxylase and Dopamine Active Transporter-Positive Neurons

<div><p>The rat is a preferred model system over the mouse for neurological studies, and cell type-specific Cre expression in the rat enables precise ablation of gene function in neurons of interest, which is especially valuable for neurodegenerative disease modeling and optogenetics. Yet, few such Cre rats are available. Here we report the characterization of two Cre rats, tyrosine hydroxylase (TH)-Cre and dopamine active transporter (DAT or Slc6a3)-Cre, by using a combination of immunohistochemistry (IHC) and mRNA fluorescence <i>in situ</i> hybridization (FISH) as well as a fluorescent reporter for Cre activity. We detected Cre expression in expected neurons in both Cre lines. Interestingly, we also found that in Th-Cre rats, but not DAT-Cre rats, Cre is expressed in female germ cells, allowing germline excision of the floxed allele and hence the generation of whole-body knockout rats. In summary, our data demonstrate that targeted integration of Cre cassette lead to faithful recapitulation of expression pattern of the endogenous promoter, and mRNA FISH, in addition to IHC, is an effective method for the analysis of the spatiotemporal gene expression patterns in the rat brain, alleviating the dependence on high quality antibodies that are often not available against rat proteins. The Th-Cre and the DAT-Cre rat lines express Cre in selective subsets of dopaminergic neurons and should be particularly useful for researches on Parkinson’s disease.</p></div

The expression of Cre recombinase recapitulates that of Th in dopaminergic neurons in the ventral tegmental area and substantia nigra.

<p>A combination of anti-TH immunostaining and Cre fluorescence <i>in situ</i> hybridization (A-A”, D-E”) as well as double fluorescence <i>in situ</i> hybridization with both Th and Cre riboprobes (B-C”) were employed to examine the co-localization of Cre mRNA and the Th gene in dopaminergic neurons of ventral tegmental area and substantia nigra. SNCD, substantia nigra compacta dorsal tier; VTA, ventral tegmental area; S probe, sense probe; AS probe, anti-sense probe.</p

The insertion of the IRES-Cre cassette into the Th locus does not change its expression pattern in the brain.

<p>(A-C) Anti-Th antibody staining in the brain of adult homozygous Th-Cre rats; (D-F”), anti-Th antibody (D, E, F) and DAT anti-sense probe <i>in situ</i> hybridization (D’, E’, F’) in the brains of wild type adult rats (D and D’) and homozygous Th-cre rats (E, E’, F and F’). AS, anti-sense; LC, locus coeruleus; OB, olfactory bulb; SNCD, substantia nigra compacta dorsal tier; SNL, the lateral part of substantia nigra; SNR, the reticular part of substantia nigra; VTA, ventral tegmental area.</p

Type II endoleaks: challenges and solutions.

Type II endoleaks are the most common endovascular complications of endovascular abdominal aortic aneurysm repair (EVAR); however, there has been a divided opinion regarding their significance in EVAR. Some advocate a conservative approach unless there is clear evidence of sac expansion, while others maintain early intervention is best to prevent adverse late outcomes such as rupture. There is a lack of level-one evidence in this challenging group of patients, and due to a low event rate of complications, large numbers of patients would be required in well-designed trials to fully understand the natural history of type II endoleak. This review will discuss the imaging, management, and outcome of patients with isolated type II endoleaks following infra-renal EVAR

The Cre recombinase in DAT-Cre rats faithfully recapitulates the expression pattern of endogenous DAT.

<p>(A-A”), anti-TH antibody and DAT RNA <i>in situ</i> hybridization on wild type rat brain sections; (B-B”), similar staining on DAT-cre homozygous rat brain sections. (C-D”), double <i>in situ</i> hybridization of Th and DAT on DAT-cre homozygous rat brain sections. AS, anti-sense probe.</p

Tdtomato labels Th positive cells in the substantia nigra area of Th-cre, Rosa Tom rat brain.

<p>(A-A”), anti-TH antibody staining was done on Rosa Tom brain sections and no live tdTomato signal could be detected; In contrast, in both SN (B-B”) and OB (C-C”), co-localization of TH antibody signal and live tdTomato signals could be observed.</p

Th-cre mediated excision of floxed allele does NOT occur in fertilized oocytes.

<p>Th-cre mediated excision of floxed allele does NOT occur in fertilized oocytes.</p

Germ line excision of floxed alleles in maternal, but not paternal, Th-Cre rat.

<p>Germ line excision of floxed alleles in maternal, but not paternal, Th-Cre rat.</p

In DAT-cre, Rosa Tom rats, only Th-positive dopaminergic neurons in the SN and VTA, but not any other cells in the brain or other adult organs, were labeled with tdTomato.

<p>(A-B”) shows overlapping signals between TH antibody staining and live tdTomato signal in the dopaminergic neurons of the SN (A-A”) and VTA (B-B”) area. In contrast, no live tdTomato signal could be detected in other brains areas such as cerebral cortex (C) and other adult organs including heart (D), kidney(E), liver (F), lung (G) and spleen (H).</p