Optimized Protocol for Imaging Cleared Neural Tissues Using Light Microscopy

Understanding physical and chemical processes at an organismal scale is a fundamental goal in biology. While science is adept at explaining biological phenomena at both molecular and cellular levels, understanding how these processes translate to organismal functions remains a challenging problem. This issue is particularly significant for the nervous system where cell signaling and synaptic activities function in the context of broad neural networks. Recent progress in tissue clearing technologies lessens the barriers that previously prevented the study of large tissue samples while maintaining molecular and cellular resolution. While these new methods open vast opportunities and exciting new questions, the logistics of analyzing cellular processes in intact tissue have to be carefully considered. In this protocol, we outline a procedure to rapidly image intact brain tissue up to thousands of cubic millimeters. This experimental pipeline involves three steps: tissue clearing, tissue imaging, and data analysis. In an attempt to streamline the process for researchers entering this field, we address important considerations for each of these stages and describe an integrated solution to image intact biological tissues. Hopefully, this optimized protocol will lower the barrier of implementing high-resolution tissue imaging and facilitate the investigations of mesoscale questions at molecular and cellular resolution

Spectroscopic Monitoring Observations of Nova V1724 Aql in 2012

Spectroscopic and photometric monitoring observations of nova Apl 2012 (V1724 Apl) were conducted at Koyama Astronomical Observatory, Fujii-Kurosaki Observatory and Bisei Astronomical Observatory. The nova was initially considered as an outbursting pre-main-sequence young stellar object. Our monitoring observations have revealed the nova to be a Fe II type classical nova. The temporal evolution of spectra and light curves of the nova were similar to those of a slow nova (e.g., V1280 Sco and V5558 Sgr). We observed no evidence of molecule formation in V1724 Aql in contrast with V2676 Oph in which dust formation occurred after the molecular formation in the nova outflow

Tumour enhancement with newly developed Mn-metalloporphyrin (HOP-9P) in magnetic resonance imaging of mice

The purpose of the study is to evaluate the tumour enhancing characteristics and biodistribution of a newly developed metalloporphyrin derivative, HOP-9P (13, 17-bis (1-carboxypropionyl) carbamoylethyl-3, 8-bis (1-phenylpropyloxyethyl)-2,7,12,18-tetra- methyl-porphynato manganese (III)). Seven mice bearing SCC VII tumours were imaged using T1-weighted conventional spin echo magnetic resonance images before and 5 min, 2 h and 24 h after intravenous injection of 0.1 mmol/kg of HOP-9P. For the acquired images, signal intensities of the tumour, muscle and oil-phantom were measured. Then, tumor/oil and tumor/muscle signal intensity ratios were calculated. Nineteen mice were sacrificed before or after the administration of HOP-9P (at 5 min, 2 h and 24 h), and the biodistribution of manganese in the tumour, muscle, liver, blood and kidneys was measured using optical emission spectrometers and was expressed as micrograms of manganese per gram of tissue. The tumour/muscle signal intensity ratio at 24 h (3.18 ± 0.34) was significantly higher than precontrast ratio (1.77 ± 0.20) (P < 0.05). The biodistribution assessment of manganese demonstrated that HOP-9P gradually and consistently accumulated in the tumour to reach the highest concentration at 24 h (3.49 ± 1.22 μ gMn/g). It is concluded that HOP-9P is a potential tumour-specific MR contrast agent. © 2001 Cancer Research Campaign http://www.bjcancer.co

HGPD: Human Gene and Protein Database, 2012 update

The Human Gene and Protein Database (HGPD; http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression and protein synthesis data. The HGPD was launched in November 2008, and 33 275 human Gateway entry clones have been constructed from the open reading frames (ORFs) of full-length cDNA, thus representing the largest collection in the world. Recently, research objectives have focused on the development of new medicines and the establishment of novel diagnostic methods and medical treatments. And, studies using proteins and protein information, which are closely related to gene function, have been undertaken. For this update, we constructed an additional 9974 human Gateway entry clones, giving a total of 43 249. This set of human Gateway entry clones was named the Human Proteome Expression Resource, known as the ‘HuPEX’. In addition, we also classified the clones into 10 groups according to protein function. Moreover, in vivo cellular localization data of proteins for 32 651 human Gateway entry clones were included for retrieval from the HGPD. In ‘Information Overview’, which presents the search results, the ORF region of each cDNA is now displayed allowing the Gateway entry clones to be searched more easily

Very early multi-color observations of the plateau phase of GRB 041006 afterglow

Observations of the optical afterglow of GRB 041006 with the Kiso Observatory 1.05 m Schmidt telescope, the Lulin Observatory 1.0 m telescope and the Xinglong Observatory 0.6 m telescope. Three-bands (B, V and R) of photometric data points were obtained on 2004 October 6, 0.025-0.329 days after the burst. These very early multi band light curves imply the existence of a color dependent plateau phase. The B-band light curve shows a clear plateau at around 0.03 days after the burst. The R band light curve shows the hint of a plateau, or a possible slope change, at around 0.1 days after the burst. The overall behavior of these multi-band light curves may be interpreted in terms of the sum of two separate components, one showing a monotonic decay the other exhibiting a rising and a falling phase, as described by the standard afterglow model.Comment: 11 pages, 2 figures, Accepted to ApJ Letter

Uptake of Radioactive Cesium by Intestinal and Probiotic Bacteria

Poster Session

Senescence marker protein 30 in acute liver failure: validation of a mass spectrometry proteomics assay

<p>Abstract</p> <p>Background</p> <p>Our previous proteomic study showed that the senescence marker protein (SMP30) is selectively present in the plasma of a murine model of acute liver failure (ALF). The aim of this study was to validate this SMP30 expression in the plasma and liver tissues of mice and humans with ALF.</p> <p>Methods</p> <p>After the proteomic analysis of plasma from a murine model of D-galactosamine/lipopolysaccharide (GalN/LPS)-induced ALF by two-dimensional electrophoresis (2-DE) and mass spectrometry, the expression levels of SMP30 in the plasma and liver tissues were validated by western blot and RT-PCR analyses. These results were then confirmed in plasma samples from humans.</p> <p>Results</p> <p>These data validate the results of 2-DE, and western blot showed that SMP30 protein levels were only elevated in the plasma of ALF mice. Further analysis revealed that GalN/LPS induced the downregulation of SMP30 protein levels in liver tissues (by approximately 25% and 16% in the GalN/LPS-treated mice and in the treated mice that survived, respectively; <it>P </it>< 0.01). Hepatic SMP30 mRNA levels decreased by about 90% only in the mice that survived the GalN/LPS treatment. Importantly, plasma obtained from patients with ALF also contained higher levels of SMP30, about (3.65 ± 0.34) times those observed in healthy volunteers.</p> <p>Conclusion</p> <p>This study shows that SMP30 is not only a potential biomarker for the diagnosis and even prognosis of ALF. It also plays a very important role in a self-protective mechanism in survival and participates in the pathophysiological processes of ALF.</p

A huge intraductal papillary mucinous carcinoma of the bile duct treated by right trisectionectomy with caudate lobectomy

<p>Abstract</p> <p>Background</p> <p>Because intraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is believed to show a better clinical course than non-papillary biliary neoplasms, it is important to make a precise diagnosis and to perform complete surgical resection.</p> <p>Case presentation</p> <p>We herein report a case of malignant IPMN-B treated by right trisectionectomy with caudate lobectomy and extrahepatic bile duct resection. Radiologic images showed marked dilatation of the left medial sectional bile duct (B4) resulting in a bulky cystic mass with multiple internal papillary projections. Duodenal endoscopic examination demonstrated very patulous ampullary orifice with mucin expulsion and endoscopic retrograde cholangiogram confirmed marked cystic dilatation of B4 with luminal filling defects. These findings suggested IPMN-B with malignancy potential. The functional volume of the left lateral section was estimated to be 45%. A planned extensive surgery was successfully performed. The remnant bile ducts were also dilated but had no macroscopic intraluminal tumorous lesion. The histopathological examination yielded the diagnosis of mucin-producing oncocytic intraductal papillary carcinoma of the bile duct with poorly differentiated carcinomas showing neuroendocrine differentiation. The tumor was 14.0 × 13.0 cm-sized and revealed no stromal invasiveness. Resection margins of the proximal bile duct and hepatic parenchyma were free of tumor cell. The patient showed no postoperative complication and was discharged on 10^thpostoperative date. He has been regularly followed at outpatient department with no evidence of recurrence.</p> <p>Conclusion</p> <p>Considering a favorable prognosis of IPMN-B compared to non-papillary biliary neoplasms, this tumor can be a good indication for aggressive surgical resection regardless of its tumor size.</p

Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics

Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed. The Gateway system is a versatile framework to construct a variety of expression clones for various experiments. We have constructed 33 275 human Gateway entry clones from full-length cDNAs, representing to our knowledge the largest collection in the world. Utilizing these clones with a highly efficient cell-free protein synthesis system based on wheat germ extract, we have systematically and comprehensively produced and analyzed human proteins in vitro. Sequence information for both amino acids and nucleotides of open reading frames of cDNAs cloned into Gateway entry clones and in vitro expression data using those clones can be retrieved from the Human Gene and Protein Database (HGPD, http://www.HGPD.jp). HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones