Special Issue on ＂Translational Omics＂

The journal Genomics Proteomics ＆ Bioinformatics （GPB） is now inviting submissions for a special issue （to be published in autumn of 2014） on the topic of＂Translational Omics＂.     

Frequent Mutation of rs13281615 and Its Association with PVT1 Expression and Cell Proliferation in Breast Cancer

The q24 band of chromosome 8 （8q24） is frequently amplified in human cancers including breast cancer, and several SNPs （single nucleotide polymorphisms） at 8q24, including rs13281615, have been identified for their association with cancer risks. These SNPs are in a ＂gene desert＂ region, and their functions in cancer development remain to be illustrated, although several of the SNPs appear to influence the genes in the ＂desert＂ in a long-range manner, including the v-myc avian myelocytomatosis viral oncogene homolog （MYC） and the non- protein coding plasmacytoma variant translocation 1 （PVT1）, both of which have been implicated in human cancers. In the current study, we examined rs13281615 for its potential role in breast cancer using normal and cancer tissues from 121 Chinese women with breast cancer. In addition to confirming the association of the GG genotype of rs 13281615 with breast cancer risk, we found that germline GG genotype was significantly associated with estrogen receptor （ER） positivity, higher tumor grade and higher proliferation index. We also found frequent somatic mutations （22/121 or 18.2%） of this SNP in breast cancer. Interestingly, the majority of the mutations （17/22 or 77%） involved a G→ A change, resulting in a decrease in the number of cancers with the GG risk genotype and subsequent loss of GG association with higher tumor grade and proliferation index in cancers. Furthermore, PVT1 expression was increased in cancers, and the increase was associated with the GG genotype of rs13281615. These results suggest that the GG genotype of SNP rs13281615 plays a role in breast cancer likely by influencing PVT1 expression, and that during oncogenesis, ＂protective＂ mutations could occur.     

Two-Body Abrasive Wear of the Surfaces of Pangolin Scales

The Pangolin, a soil-burrowing animal, is covered with scales. These scales are often abraded by soil and rock and their surface is corrugated. The abrasive wear of the surface of the scales was examined. The scales were taken from a pangolin that had died of natural causes. The tests were run on a rotary disc abrasive wear tester. The abrasive material was quartz sand （96.5 wt.%） and bentonite （3.5 wt.%）. The morphology of the abraded surfaces and the abrasion were examined by stereoscopic microscopy and scanning electron microscopy. The concepts are proposed of ＂Guiding-Effect＂ and ＂Rolling-Effect＂ on the textured surfaces under free abrasive wear conditions and the critical dimensions of the ＂Rolling-Effect＂ are discussed.     

Comparative ecogenotoxicology： Monitoring the DNA of wildlife

Ecogenotoxicology is the study of interactions between genetic material and DNA-damaging agents of anthropogenic origin in wild populations, in relation to subsequent effects on the health of organisms （Shugart and Theodorakis, 1994）. Traditionally, biomarkers for genetic toxicology can be classified in ＂biomarkers of exposure＂ and ＂biomarkers of effect＂, depending whether the aim is to monitor and quantify the exposure to genotoxicants,     

MORN motifs in plant PIPKs are involved in the regulation of subcellular localization and phospholipid binding

Multiple repeats of membrane occupation and recognition nexus （MORN） motifs were detected in plant phosphatidylinositl monophosphate kinase （PIPK）, a key enzyme in PI-signaling pathway. Structural analysis indicates that all the MORN motifs （with varied numbers at ranges of 7-9）, which shared high homologies to those of animal ones, were located at N-terminus and sequentially arranged, except those of OsPIPK1 and AtPIPK7, in which the last MORN motif was separated others by an -100 amino-acid ＂island＂ region, revealing the presence of two kinds of MORN arrangements in plant PIPKs. Through employing a yeast-based SMET （sequence of membrane-targeting） system, the MORN motifs were shown being able to target the fusion proteins to cell plasma membrane, which were further confirmed by expression of fused MORN-GFP proteins. Further detailed analysis via deletion studies indicated the MORN motifs in OsPIPK 1, together with the 104 amino-acid ＂island＂ region are involved in the regulation of differential subcellular localization, i.e. plasma membrane or nucleus, of the fused proteins. Fat Western blot analysis of the recombinant MORN polypeptide, expressed in Escherichia coli, showed that MORN motifs could strongly bind to PA and relatively slightly to PI4P and PI（4,5）P2. These results provide informative hints on mechanisms of subcellular localization, as well as regulation of substrate binding, of plant PIPKs.     

An integrated view of the correlations between genomic and phenomic variables

Genome sequencing opened the flood gate of ＂-omics＂ studies, among which the research about correlations between genomic and phenomic variables is an important part. With the development of functional genomics and systems biology, genome-wide investigation of the correlations between many genomic and phenomic variables became possible. In this review, five genomic variables, such as evolution rate （or ＂age＂ of the gene）, the length of intron and ORF （protein length） in one gene, the biases of amino acid composition and codon usage, along with the phenomic variables related to expression patterns （level and breadth） are focused on. In most cases, genes with higher mRNA/protein expression level tend to evolve slowly, have less intronic DNA, code for smaller proteins, and have higher biases of amino acid composition and codon usage. In addition, broadly expressed proteins evolve more slowly and are shorter than tissue-specific proteins. Studies in this field are helpful for deeper understanding the signatures of selection mediated by the features of gene expression and are of great significance to enrich the evolution theory.     

Introgression of Resistance to Powdery Mildew Conferred by Chromosome 2R by Crossing Wheat Nullisomic 2D with Rye

Using the nulUsomic back-cross procedure, four wheat-rye chromosome substitution 2R （2D） lines with different agronomic performance, designated WR02-145-1, WR01-145-2, WR02-145-3, and WR02-145-4, were produced from a cross between 2D nullisomic wheat （Triticum aestivum L. cv. ＂Xiaoyan 6＂） and rye （Secale cereale L. cv. ＂German White＂）. The chromosomal constitution of 2n=42=21 in WR02-145 lines was confirmed by cytological and molecular cytogenetic methods. Using genomic in situ hybridization on root tip chromosome preparations, a pair of intact rye chromosomes was detected in the WR02-145 lines. PCR using chromosome-specific primers confirmed the presence of 2R chromosomes of rye in these wheat-rye lines, indicating that WR02o145 lines are disomic chromosome substitution lines 2R （2D）. The WR02-145 lines are resistant to the powdery mildew （Erysiphe graminis DC. f. sp. tritici E. Marchal） isolates prevalent in northern China and may possess gene（s） for resistance to powdery mildew, which differ from the previously identified Pm7gene located on chromosome 2RL. The newly developed ＂Xiaoyan 6＂- ＂German White＂ 2R （2D） chromosome substitution lines are genetically stable, show desirable agronomic traits, and are expected to be useful in wheat improvement.     

Detection of food source by PCR analysis of the gut contents of Aldrichina grahami （Aldrich） （Diptera： Calliphoridae） during post-feeding period

The last meal of sarcophagous maggots may be useful in identifying the species on whose flesh they have fed （the＂host＂species）. The DNA profile of the host species may indeed be detectable in the＂last meal＂. In this paper, mitochondrial DNA analysis of gut contents was used to identify the prior host of post-feeding larvae of Aldrichina grahami （Aldrich） （Diptera： Calliphoridae）. A modified logistic equation was fitted to estimate the probability of identifying the host under five different constant temperatures （16, 20, 24, 28 and 32 ℃）. Our results shows that the detected time ranged from a maximum of 24 h at 32℃ to 42 h at 16℃ and a minimum of 12 h at 32~C to 30 h at 16℃. Furthermore, the host detection time was also calculated to give the maximal time after larval hatching from the egg. These results indicate that, in criminal cases where the maggots stray from the corpse, the last meal of the larvae should not be overlooked as potentially critical evidence.     

Mapping and quantitative trait loci analysis of verticillium wilt resistance genes in cotton

Verticillium wilt is one of the most serious constraints to cotton production in almost all of the cotton-growing countries. In this study, ＂XinLuZaol＂ （XLZl）, a susceptible cultivar Gossypium hirsutum L. and ＂Hai7124＂ （H7124）, a resistant line G. barbadense, and their F2：3 families were used to map and study the disease index induced by verticillium wilt. A total of 430 SSR loci were mapped into 41 linkage groups; the map spanned 3 745.9 cM and the average distance between adjacent loci was 8.71 cM. Four and five quantitative trait loci （QTLs） were detected based on the disease index investigated on July 22 and August 24 in 2004, respectively. These nine QTLs explained 10.63-28.83% of the phenotypic variance, six of them were located on the D sub-genome. Two QTLs located in the same marker intervals may partly explain the significant correlation of the two traits. QTLs explaining large phenotypic variation were identified in this study, which may be quite useful in cotton anti-disease breeding.     

Grasshopper （Orthoptera： Acrididae） biodiversity and grassland ecosystems

Interesting results may arise by combining studies on the structure and function of ecosystems with that of biodiversity for certain species. Grasshopper biodiversity is the result of the evolution of grassland ecosystems; however, it also impacts on the structure and the function of those ecosystems. We consider there to be a close relationship between the health of grassland ecosystems and grasshopper biodiversity. The main problems involved in this relationship are likely to include： （i） grasshopper biodiversity and its spatial pattern; （ii） the effect of grasshopper biodiversity on the ecological processes of grassland ecosystems; （iii） the biodiversity threshold of grasshopper population explosions; （iv） the relationship between grasshopper biodiversity and the natural and human factors that affect grassland ecosystems; and （v） grasshopper biodiversity and the health of grassland ecosystems. The solutions to these problems may provide sound bases for controlling disasters caused by grasshoppers and managing grassland ecosystems in the west of China. In this paper, we introduced two concepts for grasshopper biodiversity, that is, ＂spatial pattern＂ and ＂biodiversity threshold＂. It is helpful to understand the action of the spatial pattern of grasshopper biodiversity on the ecological processes of grassland ecosystems and the effect of this spatial pattern on the health of those ecosystems, owing to the fact that, in the west of China, grasslands are vast and grasshoppers are widely distributed. Moreover, we inferred that the change in the level of component richness at each type of grasshopper biodiversity can make an impact on grassland ecosystems, and therefore, there is likely to be a threshold to grasshopper biodiversity for the stability and the sustainability of those ecosystems.     

《细胞科学期刊》：研究发现脂类代谢调控新机制

来自中国科学院遗传与发育生物学研究所，德国马普生物物理化学研究所的研究人员发表了题为＂Opposite and redundant roles of the two Drosophila Perilipins in lipid mobilization ＂ 的文章。发现了果蝇中仅有的两个PAT家族蛋白Plinl和Plin2对脂解既有相同。又有相反的调控功能。揭示了果蝇PAT家族蛋白在脂解中的复杂功能。为后续解析PAT家族蛋白在进化上的功能提供了有力的理论依据。相关成果公布在《细胞科学期TIJ）（Journal of CellScience）上。     

A GIM-Based Biomimetic Learning Approach for Motion Generation of a Multi-Joint Robotic Fish

In this paper, we propose a biomimetic learning approach for motion generation of a multi-joint robotic fish. Based on a multi-joint robotic fish model, two basic Carangiform swimming patterns, namely ＂cruise＂ and ＂C sharp turning＂, are extracted as training samples from the observations of real fish swimming. A General Internal Model （GIM）, which is an imitation of Central Pattern Generator （CPG） in nerve systems, is adopted to learn and to regenerate coordinated fish behaviors. By virtue of the universal function approximation ability and the temporal/spatial scalabilities of GIM, the proposed learning approach is able to generate the same or similar fish swimming patterns by tuning two parameters. The learned swimming patterns are implemented on a multi-joint robotic fish in experiments. The experiment results verify the effectiveness of the biomimetic learning approach in generating and modifying locomotion patterns for the robotic fish.     

Systems Biology Brings Life Sciences Closer——Report on the China-UK Systems Biology Workshop 2005

The China-UK Systems held during June 20-21 Biology Workshop 2005 was in the National Science Park of Zhejiang University, Hangzhou, China. It was organized by the Institute of Bioinformatics, Zhejiang University, and was initiated by Prof. Dr. Jun Zhu （Zhejiang University） and Prof. Dr. John Findlay （University of Leeds, UK）. The workshop was part of the program called UK-China Partners in Science, a one-year campaign that was initiated by the British government to explore more collaborations between UK and China on science and technology. It was attended also by a representative of this program, Mr. Frank Yuan, senior science ＆ innovation officer. The idea of the workshop was to bring together experts with specialists in systems biology in order to promote the ＂natural partnership＂ between scientists from the two countries. The most important items of systcms biology considered at the workshop were： （1） New technologies and advances in systems biology; （2） Research developments in genomics and proteomics; （3） New methodologies and software in computational biology; （4） Research collaboration on systems biology between China and UK.     

The Drosophila ovary： an active stem cell community

The authors want to change the Cover Caption of Cell Research, Volume 17, Issue 1. The corrected Cover Caption should be＂ Germline stem cells （green dots） at the tip of the Drosophila ovariole generate the germline cells of the egg chambers （large blue circles denote nurse cells）. See page 15-25 for more details.＂     

The construction of a genetic linkage map of non-heading Chinese cabbage （Brassica campestris ssp. chinensis Makino）

Non-heading Chinese cabbage （Brassica carnpestris ssp. chinensis Makino） is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid （DH） lines, and the DH population was derived from a commercial hybrid ＂Hanxiao＂ （lines SW-13 x L-118）. Out of the 614 polyrnorphic markers, 43.49% were not assigned to any of the linkage groups （LGs）. Chi-square tests showed that 42.67% markers were distorted from expected Mendelian segregation ratios, and the direction of distorted segregation was mainly toward the paternal parent L-118. After sequentially removing the markers that had an interval distance smaller than 1 cM from the upper marker, the overall quality of the linkage map was increased. Two hundred and sixty-eight molecular markers were mapped into 10 LGs, which were anchored to the corresponding chromosome of the B. rapa reference map based on com- mon simple sequence repeat （SSR） markers. The map covers 973.38 cM of the genome and the average interval distance between markers was 3.63 cM. The number of markers on each LG ranged from 18 （R08） to 64 （R07）, with an average interval distance within a single LG from 1.70 cM （R07） to 6.71 cM （R06）. Among these mapped markers, 169 were sequence-related amplified polymorphism （SRAP） molecular markers, 50 were SSR markers and 49 were random amplification polymorphic DNA （RAPD） markers. With further saturation to the LG9 the current map offers a genetic tool for loci analysis for important agronomic traits.     

An evaluation of garlic lectin as an alternative carrier domain for insecticidal fusion proteins

The mannose-binding lectin GNA （snowdrop lectin） is used as a＂carrier＂ domain in insecticidal fusion proteins which cross the insect gut after oral ingestion. A similar lectin from garlic bulb, ASAII, has been evaluated as an alternative ＂carrier＂. Recombinant ASAII delivered orally to larvae of cabbage moth （Mamestra brassica; Lepidoptera） was subsequently detected in haemolymph, demonstrating transport. Fusion proteins comprising an insect neurotoxin, ButaIT （Buthus tamulus insecticidal toxin; red scorpion toxin） linked to the C-terminal region of ASAII or GNA were produced as recombinant proteins （GNA/ ButaIT and ASA/ButaIT） by expression in Pichia pastoris. In both cases the C-terminal sequence of the lectin was truncated to avoid post-translational proteolysis. The GNA- containing fusion protein was toxic by injection to cabbage moth larvae （LD50≈ 250μg/g）, and when fed had a negative effect on survival and growth. It also decreased the survival of cereal aphids （Sitobion avenae; Homoptera） from neonate to adult by 〉70% when fed. In contrast, the ASA-ButaIT fusion protein was non-toxic to aphids, and had no effect on lepidopteran larvae, either when injected or when fed. However, intact ASA-ButaIT fusion protein was present in the haemolymph of cabbage moth larvae following ingestion, showing that transport of the fusion had occurred. The stabilities of GNA/ButaIT and ASA/ButaIT to proteolysis in vivo after injection or ingestion differed, and this may be a factor in determining insecticidal activities.     

飞利浦Practix 33 plus床边X线机曝光无射线故障检修

＂Lack of X-ray＂是Practix 33 plus（P33）床边机常见故障,它的原因是多方面的。本文结合本机工作原理框图,并通过几个实例总结出一套快速准确判断故障点的方法。     

Effects of Acetylcholine, Cytochalasin B and Amiprophosmethyl on Phloem Transport in Radish （Raphanus sativas）

We investigated the role of the ＂sieve tube-companion cell complex＂ lining the tube periphery, particularly the microfilament and microtubule, in assisting the pushing of phloem sap flow. We made a simple phloem transport system with a living radish plant, in which the conducting channel was exposed for local treatment with chemicals that are effective in modulating protoplasmic movement （acetylcholine, （ACh） a neurotransmitter in animals and insects; cytochalasin B, （CB） a specific inhibitor of many cellular responses that are mediated by microfilament systems and amiprophos-methyl, （APM） a specific inhibitor of many cellular responses that are mediated by microtubule systems）. Their effects on phloem transport were estimated by two experimental devices： （i） a comparison of changes in the amount of assimilates in terms of carbohydrates and ^14C-labeled photosynthetic production that is left in the leaf blade of treated plants; and （ii） distribution patterns of ^14C-labeled leaf assimilates in the phloem transport system. The results indicate that CB and APM markedly inhibited the transfer of photosynthetic product from leaf to root via the leaf vein, while ACh enhanced the transfer of photosynthetic product in low concentrations （5.0×10^-4 mol/L） but inhibited it in higher concentrations （2.0×10^-3 mol/L） from leaf to root via the leaf vein. Autoradiograph imaging clearly reveals that ACh treatment is more effective than the control, and both CB and APM treatments effectively inhibit the passage of radioactive assimilates. All of the results support the postulation that the peripheral protoplasm in the sieve tube serves not only as a passive semi-permeable membrane, but is also directly involved in phloem transport.     

A Novel ABA Insensitive Mutant of Lotus japonicus with a Wilty Phenotype Displays Unaltered Nodulation Regulation

An ABA insensitive mutant, Beyma, was isolated in Lotus japonicus MG-20 from an EMS mutagenesis population using root growth inhibition to applied ABA as the screening criterion. （The name ＂Beyma＂ was taken from the Australian Aboriginal language, Wagiman, beyma, meaning ‘drying up＇.） The stable mutant that segregates as a dominant Mendelian mutation is insensitive to ABA induced inhibition of germination, vegetative growth, stomatal opening, as well as nodulation. Tissue ABA levels were normal, suggesting a sensitivity rather than biosynthesis mutation. It is slow-growing （50-70% of wild-type MG-20） and has a near-constitutive wilty phenotype associated with its inability to regulate stomatal opening. Whilst showing a wide range of ABA insensitive phenotypes, Beyma did not show alteration of nodule number control, as, in the absence of added ABA, the number and patterning （but not size） of nodules formed in the mutant were similar to that of MG-20. Split root experiments on MG-20 showed that application of ABA on one side of the root inhibited nodulation locally but not systemically. We propose that ABA is not involved directly in systemic autoregulation of nodulation （AON）.