Simple outlier detection for a multi-environmental field trial

The aim of plant breeding trials is often to identify crop variety that are well adapt to target environments. These varieties are identified through genomic prediction from the analysis of multi-environmental field trial (MET) using linear mixed models. The occurrence of outliers in MET is common and known to adversely impact the accuracy of genomic prediction yet the detection of outliers are often neglected. A number of reasons stand for this—first, complex data such as a MET give rise to distinct levels of residuals (eg, at a trial level or individual observation level). This complexity offers additional challenges for an outlier detection method. Second, many linear mixed model software packages that cater for complex variance structures needed in the analysis of MET are not well streamlined for diagnostics by practitioners. We demonstrate outlier detection methods that are simple to implement in any linear mixed model software packages and computationally fast. Although these methods are not optimal methods in outlier detection, they offer practical value for ease of application in the analysis pipeline of regularly collected data. These are demonstrated using simulation based on two real bread wheat yield METs. In particular, models that consider analysis of yield trials either independently or jointly (thus borrowing strength across trials) are considered. Case studies are presented to highlight benefit of joint analysis for outlier detection.     

Expression of the human salivary alpha-amylase gene in yeast and characterization of the secreted protein

Recombinant plasmids were constructed in which the human salivary alpha-amylase gene, with or without the N-terminal signal sequence for secretion, was placed under control of the APase (PHO5) promoter of Saccharomyces cerevisiae. In yeast cells transformed with the alpha-amylase gene having the human signal sequence for secretion, the gene was expressed and the enzyme was secreted into the medium in three different glycosylated forms. The amylase gene without the signal sequence was also expressed in yeast, but the products were neither secreted nor glycosylated. Determination of the N-terminal amino acid (aa) sequence revealed that the 15-aa signal sequence had been cleaved from the secreted enzyme, and that the N-terminal residue, glutamine, had been modified into pyroglutamate, as is commonly observed with the mammalian salivary alpha-amylase. Thus, the human salivary alpha-amylase signal sequence for secretion was correctly recognized and processed by the yeast secretory pathway. The C-terminal residue was identified as leucine, which is predicted from the nucleotide sequence data to be located at position 511 in front of the termination codon. Therefore, there is no post-translational processing in formation of the C terminus.     

Formation of a stable l-ascorbic acid α-glucoside by mammalian α-glucosidase-catalyzed transglucosylation

Enzymatic transglucosylation from maltose to l-ascorbic acid (AA) with mammalian tissue homogenates was determined by a high-performance liquid chromatography method and compared with the reaction catalyzed by α-glucosidase from Aspergillus niger. The homogenates of small intestine and kidney had a high transglucosylase activity to form a new type of glucosylated AA, which was associated with α-glucosidase activity. The new compound was demonstrated to be an equimolar conjugate of AA and glucose by the spectral and quantitative analyses. In particular, it showed a high stability in a neutral solution and no reducing activity toward cytochrome c and a dye. These properties were very different from those of AA and l-ascorbic acid α-glucoside formed with α-glucosidase form A. niger, but they were consistent with those of l-ascorbic acid 2-O-phosphate and l-ascorbic acid 2-O-sulfate. Moreover, it exhibited a reducing power associated with AA after mild acid hydrolysis or treatment with rat intestinal α-glucosidase. These results indicate that it should be assigned the 2-O-α-glucoside structure. Consequently, i should be assigned the 2-O-α-glucoside structure. Consequently, it is concluded that mammalian α-glucosidase is able to form a very stable and nonreducing form of glucosylated AA through a specific transglucosylation reaction distinct from that of microbial α-glucosidase.     

Site-targeted non-viral gene delivery by direct DNA injection into the pancreatic parenchyma and subsequent in vivo electroporation in mice

The pancreas is considered an important gene therapy target because the organ is the site of several high burden diseases, including diabetes mellitus, cystic fibrosis, and pancreatic cancer. We aimed to develop an efficient in vivo gene delivery system using non-viral DNA. Direct intra-parenchymal injection of a solution containing circular plasmid pmaxGFP DNA was performed on adult anesthetized ICR female mice. The injection site was sandwiched with a pair of tweezer-type electrode disks, and electroporated using a square-pulse generator. Green fluorescent protein (GFP) expression within the injected pancreatic portion was observed one day after gene delivery. GFP expression reduced to baseline within a week of transfection. Application of voltages over 40 V resulted in tissue damage during electroporation. We demonstrate that electroporation is effective for safe and efficient transfection of pancreatic cells. This novel gene delivery method to the pancreatic parenchyma may find application in gene therapy strategies for pancreatic diseases and in investigation of specific gene function in situ.     

Vitronectin secretion by hepatic and non-hepatic human cancer cells

Summary Thirty-eight human cancer cell lines and subclones derived from 12 different organs were screened for vitronectin secretion in their culture media. By immunoblotting analysis we detected high secretion by three out of five hepatoma cell lines tested but no secretion by the others. In addition, significant secretion was observed in seven non-hepatic cancer cell lines and subclones derived from the cervix, lung, and pancreas. These vitronectin-secreting cells included PLC/PRF/5, HuH-6 #5, HuH-7, HeLa S3, HeLa · P3 #2, #3, #6, #8, A549, and MIAPaCa-2. The results were further confirmed by quantitative analysis using sandwich enzyme-linked immunoassay, and activity analysis of cell attachment promotion on Western blotted filters.     

Bioactive jatrophane diterpenes from Euphorbia guyoniana

Chromatographic investigation of the methylenechloride/methanol extract of the aerial parts of Euphorbia guyoniana afforded two jatrophane diterpenes, designated guyonianins E and F, in addition to a known jatrophane diterpene. The structures of the compounds were determined by comprehensive NMR analyses, including DEPT, COSY, HMQC, HMBC, NOESY and HRMS. These compounds exhibited cytotoxicity against human embryonic kidney 293 (HEK293) cells with IC₅₀ values of 35–100 μM.     

Fish otolith contains a unique structural protein, otolin-1.

A collagen-like protein was identified from the otoliths of the chum salmon, Oncorhynchus keta. The otolith, composed mainly of calcium carbonate with small amount of organic matrices, is formed in the inner ear and serves as a part of the hearing and balance systems. Although the organic matrices may play important roles in the growth of otolith, little is known about their chemical nature and physiological function. In this study, a major organic component of the otolith, designated otolin-1, which may serve as a template for calcification, was purified. The sequences of two tryptic peptides from otolin-1 revealed high homology with parts of a saccular collagen which had been described previously [Davis, J.G., Oberholtzer, J.C., Burns, F.R. & Greene, M.I. (1995) Science 267, 1031-1034]. Cloning of a cDNA coding for otolin-1 revealed that the deduced amino-acid sequence contained a collagenous domain in the central part of the protein. Although collagen is the most abundant structural protein in the animal body, otolin-1 mRNA was expressed specifically in the sacculus. Immunohistochemical studies showed that otolin-1 is synthesized in the transitional epithelium and transferred to the otolith and otolithic membrane. This is the first report concerning characterization of a structural protein containing many tandem repeats of the sequence, Gly-Xaa-Yaa, typical for collagen from the biomineral composed of calcium carbonate.     

The synthesis and biodistribution of [11C]metformin as a PET probe to study hepatobiliary transport mediated by the multi-drug and toxin extrusion transporter 1 (MATE1) in vivo

In order to develop a new positron emission tomography (PET) probe to study hepatobiliary transport mediated by the multi-drug and toxin extrusion transporter 1 (MATE1), ¹¹C-labelled metformin was synthesized and then evaluated as a PET probe. [¹¹C]Metformin ([¹¹C]4) was synthesized in three steps, from [¹¹C]methyl iodide. Evaluation by small animal PET of [¹¹C]4 showed that there was increased concentrations of [¹¹C]4 in the livers of mice pre-treated with pyrimethamine, a potential inhibitor of MATEs, inhibiting the hepatobiliary excretion of metformin. Radiometabolite analysis showed that [¹¹C]4 was not degraded in vivo during the PET scan. Biodistribution studies were undertaken and the organ distributions were extrapolated into a standard human model. In conclusion, [¹¹C]4 may be useful as a PET probe to non-invasively study the in vivo function of hepatobiliary transport and drug–drug interactions, mediated by MATE1 in future clinical investigations.     

Heat denaturation increases the sensitivity of the cytomegalovirus loop‐mediated isothermal amplification method

A new protocol for CMV LAMP with an additional heat denaturation step was developed. While the sensitivity of the original CMV LAMP method was 500 copies/tube, sensitivity was increased by up to 100 copies/tube by additional heat denaturation. CMV DNA was detected in 103 of 350 samples (29.4%) by the original CMV LAMP procedure and 148 of 350 samples (42.3%) by the new CMV LAMP protocol. When the pp65 antigenemia assay was used as the standard method, the sensitivity, specificity, PPV, and NPV of the new protocol were 92.9%, 77.7%, 62.2%, and 96.5%, respectively.