近红外光谱分析在中国伞形科阿魏亚植物分类中的应用

探讨了近红外光谱分析技术在中国伞形科阿魏亚族植物分类中的应用。使用样本近红外光谱之间的有正切值作为聚类统计量,用最短距离法对１４种阿魏亚族植物样本的近红外光谱数据进行聚类分析,结果与传统植物学分类较为接近。     

Long Fluorescence Lifetime Molecular Probes Based on Near Infrared Pyrrolopyrrole Cyanine Fluorophores for In Vivo Imaging

Fluorescence lifetime (FLT) properties of organic molecules provide a new reporting strategy for molecular imaging in the near infrared (NIR) spectral region. Unfortunately, most of the NIR fluorescent dyes have short FLT typically clustered below 1.5 ns. In this study, we demonstrate that a new class of NIR fluorescent dyes, pyrrolopyrrole cyanine dyes, have exceptionally long FLTs ranging from 3 to 4 ns, both in vitro (dimethyl sulfoxide and albumin/water solutions) and in vivo (mice). These results provide a new window for imaging molecular processes, rejecting backscattered light and autofluorescence, and multiplexing imaging information with conventional NIR fluorescent dyes that absorb and emit light at similar wavelengths.     

Deletion of clustered O-linked carbohydrates does not impair function of low density lipoprotein receptor in transfected fibroblasts

A single exon in the gene for the receptor for plasma low density lipoprotein (LDL) encodes a region of clustered serine and threonine residues that is immediately external to the membrane-spanning sequence. This region has been proposed as the site of clustered O-linked carbohydrate chains. In the current studies we have deleted the 144 base pairs (48 amino acids) that encode this serine- and threonine-rich region from the cDNA for the human LDL receptor. Upon transfection into receptor-deficient hamster fibroblasts, this mutated cDNA encoded a shortened receptor that no longer showed an anomalously high molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Labeling with [3H]glucosamine confirmed the lack of clustered O-linked sugars and further revealed that the shortened receptor and the normal receptor both contained isolated O-linked carbohydrate chains attached to the NH2-terminal portion of the protein. The ratio of clustered to isolated O-linked sugar chains in the normal receptor was estimated to be approximately 4-6 to 1. Despite the loss of clustered O-linked carbohydrate, the LDL receptor encoded by the deletion-bearing cDNA bound and internalized LDL normally. It also recycled normally and exhibited a normal half-life. We conclude that: 1) the serine- and threonine-rich region of the LDL receptor is the site for addition of clustered O-linked carbohydrates; 2) the receptor contains a small number of isolated chains of O-linked carbohydrates in addition to the clustered chains; and 3) the clustered O-linked carbohydrates are not essential for LDL receptor function in cultured hamster fibroblasts.     

The apolipoprotein L gene cluster has emerged recently in evolution and is expressed in human vascular tissue

We previously isolated APOL3 (CG12-1) cDNA and now describe the isolation of APOL1 and APOL2 cDNA from an activated endothelial cell cDNA library and show their endothelialspecific expression in human vascular tissue. APOL1-APOL4 are clustered on human chromosome 22q13.1, as a result of tandem gene duplication, and were detected only in primates (humans and African green monkeys) and not in dogs, pigs, or rodents, showing that this gene cluster has arisen recently in evolution. The specific tissue distribution and gene organization suggest that these genes have diverged rapidly after duplication. This has resulted in the emergence of an additional signal peptide encoding exon that ensures secretion of the plasma high-density lipoprotein-associated APOL1. Our results show that the APOL1-APOL4 cluster might contribute to the substantial differences in the lipid metabolism of humans and mice, as dictated by the variable expression of genes involved in this process.     

Isolation and characterization of cDNA clones for chicken major histocompatibility complex class II molecules

The chicken major histocompatibility complex (MHC), the B complex, is being intensively analysed at the DNA level. To further probe the molecular structure of chicken MHC class II genes, cDNA clones coding for chicken MHC class II (B-L) p chain molecules were isolated from an inbred G-B2 Leghorn chicken spleen and liver. Twenty-nine cDNA clones were isolated from the spleen and eight cDNA clones were isolated from the liver. Based on restriction maps, most clones could be clustered into one family of genes. Four cDNA clones were sequenced (S7, S10 and S19 from the spleen and L1, which was identical to S19, from the liver). Complete amino acid sequences of B-Lβ chain molecules were predicted from the nucleotide sequences of the cDNA clones. Although both the nature and the location of the conserved residues were similar in chicken and mammalian sequences, some species-specific differences were found, suggesting that the structures of the B-L molecules of this haplotype are similar, but not identical, to their mammalian counterparts.     

Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences

MOTIVATION: In the previous works, we developed ATGpr, a computer program for predicting the fullness of a cDNA, i.e. whether it contains an initiation codon or not. Statistical information of short nucleotide fragments was fully exploited in the prediction algorithm. However, sequence similarities to known proteins, which are becoming increasingly available due to recent rapid growth of protein database, were not used in the prediction. In this work, we present a new prediction algorithm based on both statistical and similarity information, which provides better performance in sensitivity and specificity. RESULTS: We evaluated the accuracy of ATGpr for predicting fullness of cDNA sequences from human clustered ESTs of UniGene, and we obtained specificity, sensitivity, and correlation coefficient of this prediction. Specificity and sensitivity crossed at 46% over the ATGpr score threshold of 0.33 and the maximum correlation coefficient of 0.34 was obtained at this threshold. Without ATGpr we found it effective to use alignments with known proteins for predicting the fullness of cDNA sequences. That is, specificity increased monotonously as similarity (identity of the alignments) increased. Specificity was achieved greater than 80% if identity was greater than 40%. For more effective prediction of fullness of cDNA sequences we combined the similarity (identity of query sequence) with known proteins and ATGpr score. As a result, specificity became greater than 80% if identity was greater than 20%. AVAILABILITY: The prediction program, called ATGpr_ sim, is available at http://www.hri.co.jp/atgpr/ATGpr_sim.html CONTACT: nisikawa@crl.hitachi.co.jp     

New estimation method for fatty acid composition in oil using near infrared spectroscopy

The absorption bands of cis-unsaturation and the carbon chain length of the fatty acid moieties in oil appear in the near infrared (NIR) wavelength region, especially around 1600-1800 nm. Using this region, a new estimation method for fatty acid composition analysis is proposed. Because the differences of the original NIR spectra are miniscule even in this region, the second derivative NIR spectra were examined in order to estimate the fatty acid composition in oil exclusively from the spectral patterns obtained. The parameters for calculating the second derivative NIR spectra were examined to make the spectral difference clearer. In any parameter, the absorption band was shifted to the shorter wavelength region when the unsaturation in fatty acid moieties increased, and it was shifted to the longer wavelength region when the carbon chain length increased. When the parameters were correct, this NIR method can estimate the fatty acid composition roughly, but simply, easily, and sometimes nondestructively.     

暴马丁香不同种源种子和幼苗的表型性状变异及其与地理-气候因子的相关性

为探究不同产地暴马丁香﹝Syringa reticulata subsp. amurensis ( Rupr.) P. S. Green et M. C. Chang〕种子和幼苗的表型性状变异规律及其与地理-气候因子的关系,以来源于黑龙江、河北、北京、内蒙古、青海和山西的10个种源(包括6个野生种源和4个栽培种源)的种子和幼苗为实验材料,对种子长和宽、种翅长和宽、百粒质量、发芽率、叶长和宽、叶长与叶宽的比值、叶柄长、株高和地径12个表型性状进行测量;在此基础上,进行了方差分析、变异系数分析、主成分分析、聚类分析及相关性分析。结果显示：暴马丁香不同种源间种子和幼苗的表型性状均有极显著差异(P=0.01),差异较大的表型性状为发芽率、百粒质量、种翅长和种翅宽。种源内和种源间各表型性状的变异系数(CV)均差异较大,种源内CV值为1.39%~45.56%,种源间CV值为6.45%~42.76%;其中,种源内种翅长和种翅宽的CV平均值较大,发芽率和百粒质量的CV平均值均较小,而种源间发芽率和百粒质量的CV值则较大。主成分分析结果表明：暴马丁香表型性状间的差异主要体现在种子长、种子宽和叶长,其次为株高、发芽率、地径、叶宽和种翅宽。根据聚类分析结果,供试的10个种源被划分为4类,其中,来源于北京和内蒙古及3个来源于河北的种源聚为Ⅰ类,来源于黑龙江哈尔滨的2个种源聚为Ⅱ类,来源于山西的2个种源聚为Ⅲ类,来源于青海的1个种源单独聚为Ⅳ类,聚类结果与各种源的地理分布有关。相关性分析结果表明：各表型性状间及表型性状与地理-气候因子间均存在不同的相关性,其中,种子发芽率与种子的其他5个表型性状均无显著相关性;经度和纬度与各表型性状均无显著相关性,而海拔、年均温和无霜期则是影响表型性状变异的主要因子。综合分析结果显示：暴马丁香各种源间存在明显的地理遗传分化,地理隔离和生态因子的大幅变化导致其种子和幼苗的表型性状变异丰富。根据研究结果,对暴马丁香的保护和利用提出了一些建议。     

Extraordinarily high density of unrelated genes showing overlapping and intraintronic transcription units

The cloning of pyrroline 5-carboxylate reductase from Drosophila melanogaster was accomplished by cDNA complementation of an Escherichia coli proline auxotroph. The corresponding P5cr gene is tightly clustered with three other expressed coding regions. A bidirectional promoter, an overlapping 3'UTR and an intraintronic sequence may all be found in only 4.3 kb, making this the most densely clustered region of unrelated genes in any eukaryote.     

Major oxidative products of cytosine are substrates for the nucleotide incision repair pathway

Most common point mutations occurring spontaneously or induced by ionizing radiation are C-->T transitions implicating cytosine as the target. Oxidative cytosine derivatives are the most abundant and mutagenic DNA damage induced by oxidative stress. Base excision repair (BER) pathway initiated by DNA glycosylases is thought to be the major pathway for the removal of these lesions. However, in alternative nucleotide incision repair (NIR) pathway the apurinic/apyrimidinic (AP) endonucleases incise DNA duplex 5' to an oxidatively damaged base in a DNA glycosylase-independent manner. Here, we characterized the substrate specificity of human major AP endonuclease, Ape1, towards 5-hydroxy-2'-deoxycytidine (5ohC) and alpha-anomeric 2'-deoxycytidine (alphadC) residues. The apparent kinetic parameters of the reactions suggest that Ape1 and the DNA glycosylases/AP lyases, hNth1 and hNeil1 repair 5ohC with a low efficiency. Nevertheless, due to the extremely high cellular concentration of Ape1, NIR was the major activity towards 5ohC in cell-free extracts. To address the physiological role of NIR function, we have characterized naturally occurring Ape1 variants including amino acids substitutions (E126A, E126D and D148E) and N-terminal truncated forms (NDelta31, NDelta35 and NDelta61). As expected, all Ape1 mutants had proficient AP endonuclease activity, however, truncated forms showed reduced NIR and 3'-->5' exonuclease activities indicating that these two functions are genetically linked and governed by the same amino acid residues. Furthermore, both Ape1-catalyzed NIR and 3'-->5' exonuclease activities generate a single-strand gap at the 5' side of a damaged base but not at an AP site in duplex DNA. We hypothesized that biochemical coupling of the nucleotide incision and exonuclease degradation may serve to remove clustered DNA damage. Our data suggest that NIR is a backup system for the BER pathway to remove oxidative damage to cytosines in vivo.     

Stability across environments of the coffee variety near infrared spectral signature

Previous study on food plants has shown that near infrared (NIR) spectral methods seem effective for authenticating coffee varieties. We confirm that result, but also show that inter-variety differences are not stable from one harvest to the next. We put forward the hypothesis that the spectral signature is affected by environmental factors. The purpose of this study was to find a way of reducing this environmental variance to increase the method's reliability and to enable practical application in breeding. Spectral collections were obtained from ground green coffee samples from multilocation trials. Two harvests of bean samples from 11 homozygous introgressed lines, and the cv 'Caturra' as the control, supplied from three different sites, were compared. For each site, squared Euclidean distances among the 12 varieties were estimated from the NIR spectra. Matrix correlation coefficients were assessed by the Mantel test. We obtained very good stability (high correlations) for inter-variety differences across the sites when using the two harvests data. If only the most heritable zones of the spectrum were used, there was a marked improvement in the efficiency of the method. This improvement was achieved by treating the spectrum as succession of phenotypic variables, each resulting from an environmental and genetic effect. Heritabilities were calculated with confidence intervals. A near infrared spectroscopy signature, acquired over a set of harvests, can therefore effectively characterize a coffee variety. We indicated how this typical signature can be used in breeding to assist in selection.     

Forensic visualization of foreign matter in human tissue by near-infrared spectral imaging: methodology and data mining strategies.

BACKGROUND: Rapidity of data acquisition, high image fidelity and large field of view are of tremendous value when looking for chemical contaminants or for the proverbial "needle in the haystack" - in this case foreign inclusions in histologic sections of biopsy or autopsy tissues. Near infrared chemical imaging is one of three chemical imaging techniques (NIR, MIR and Raman) based on vibrational spectroscopy, and provides distinct technical advantages for this application. METHODS: We have chosen to utilize and evaluate near infrared (NIR) imaging for studies of foreign materials in tissue because the experimental configuration is relatively simple, data collection is rapid, and large sample areas can be screened with high image fidelity and spatial resolution. RESULTS: We have shown that NIR imaging can readily find and identify silicone gel inclusions in biological tissue samples. Additionally, preliminary results indicate that spectral signatures in the data set are also potentially sensitive to structural changes in the surrounding tissue that may be induced by the foreign body. CONCLUSIONS: NIR chemical imaging is a powerful, non-destructive tool for localization and identifying foreign contaminants in biological tissue. Preliminary results indicate that NIR imaging is also sensitive enough to differentiate tissue types (perhaps based on collagen structural differences), and provide data on the spatial localization of these components.