Integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression

Mass spectrometry(MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular metabolic phenotypes.The metabolomes of cells,tissues,and organisms comprise a variety of molecules including lipids,amino acids,sugars,organic acids,and so on.Metabolomics mainly focus on the hydrophilic classes,while lipidomics has emerged as an independent omics owing to the complexities of the organismal lipidomes.The potential roles of lipids and small metabolites in disease pathogenesis have been widely investigated in various human diseases,but system-level understanding is largely lacking,which could be partly attributed to the insufficiency in terms of metabolite coverage and quantitation accuracy in current analytical technologies.While scientists are continuously striving to develop high-coverage omics approaches,integration of metabolomics and lipidomics is becoming an emerging approach to mechanistic investigation.Integration of metabolome and lipidome offers a complete atlas of the metabolic landscape,enabling comprehensive network analysis to identify critical metabolic drivers in disease pathology,facilitating the study of interconnection between lipids and other metabolites in disease progression.In this review,we summarize omics-based findings on the roles of lipids and metabolites in the pathogenesis of selected major diseases threatening public health.We also discuss the advantages of integrating lipidomics and metabolomics for in-depth understanding of molecular mechanism in disease pathogenesis.     

DCCP and DICP： Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins

Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases （DCCP and DICP） containing the known copper- and iron-chelating proteins~ which are freely available from the website http：//sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.     

Comparison of alginate and “Pesta” for formulation of Phanerochaete chrysosporium

Summary Alginate and wheat gluten (Pesta) matrices were compared for the encapsulation of the white rot fungus Phanerochaete chrysosporium. Pesta granules were not successful for formulating P. chrysosporium although control granules made with Alternaria alternata yielded viable fungal colonies; the gluten in wheat flour apparently inhibits growth of the white rot fungus. P. chrysosporium formulated in alginate with corncob grits or sawdust, and stored at room temperature, yielded over 50% viability of encapsulated mycelia after six months. Alginate encapsulation offers a promising technology for the delivery of white rot fungi to toxic waste sites.     

First Announcement of and Call for Papers for ＂Forum on Genetics Progress and Human Health＂

＂Forum on Genetics Progress and Human Health＂ will be held at Yunnan University in Kunming, Yunnan Province, China, in November, 2007. The forum focuses on the current progress and future directions in all major aspects of human genetics and medical genetics. The submitted papers written in English will be considered for publication in Journal of Genetics and Genomics after peer-review and papers in Chinese in Hereditas （Beijing）. Papers＇ in the following areas are encouraged for submission and outstanding papers will be selected for oral presentation in the forum.     

First Announcement of and Call for Papers for ＂Forum on Genetics Progress and Human Health＂

＂Forum on Genetics Progress and Human Health＂ will be held at Yunnan University in Kunming, Yunnan Province, China, in November, 2007. The forum focuses on the current progress and future directions in all major aspects of human genetics and medical genetics. The submitted papers written in English will be considered for publication in Journal of Genetics and Genomics after peer-review and papers in Chinese in Hereditas （Beijing）. Papers in the following areas are encouraged for submission and outstanding papers will be selected for oral presentation in the forum.     

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as “marker” genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa.We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for “all bacteria and archaea”, 114 for “all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.     

Isolation and characterization of cDNA clones for α- and β-subunits of ovine luteinizing hormone

A cDNA library of ovine pituitary DNA in plasmid pBR322 has been constructed by conventional methods with certain modifications. The library was screened using partial cDNAs for ratα-subunit and LHβ. We have isolated cDNA clones for ovineα-subunit and LHβ. The identification of these clones was confirmed by partial sequencing. The clones bear about 80% sequence homology with the respective rat cDNAs in the sequenced regions and hybridize with the rat clones in 5 X SSC at 55°C. The ovine LHβ clone has an insert of about 650 bp and selects an RNA of about 750 bases in a northern blot. The α-subunit cDNA clone has an insert of about 550 bp; it has two internalPst I sites and thus shows restriction-based differences from ratα-subunit cDNA, which does not have anyPst I site.     

Development and Evaluation of Intron and Insertion–Deletion Markers for Gossypium barbadense

A total of 588 Gossypium barbadense coding sequences (CDSs) from nucleotide databases were selected for marker development. After selection, 125 CDSs were used to design 126 markers, including 39 intron polymorphisms (GbIPs) and 87 insertion?Cdeletion polymorphisms (GbIDPs). These markers were evaluated by analyzing the genetic diversity of 66 tetraploid cotton accessions including 56 G. barbadense accessions and 10 Gossypium hirsutum accessions. The amplification efficiencies of the GbIPs and GbIDPs were 0.560 and 0.489 for polymorphism information content, 0.744 and 0.690 for effective multiplex ratio (E), 0.653 and 0.438 for qualitative of nature of data, and 0.272 and 0.148 for effective marker index. Principal coordinate analysis showed profound differences between G. hirsutum and G. barbadense accessions. In addition, most of the G. barbadense accessions of Xinjiang, China were clearly different from foreign and other Chinese G. barbadense accessions. The 126 markers were also evaluated for their ability to enrich genetic maps, and 16 polymorphic loci were mapped on nine chromosomes with six loci on A subgenome and 10 loci on D subgenome. The mapping efficiencies of GbIPs and GbIDPs primers were 15.38% and 11.49%, respectively. This study well proves that GbIPs and GbIDPs can be successfully applied to the analysis of genetic diversity and construction of genetic maps.     

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

Background  

High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.     

Seed dispersal and colonization ability of plants — Assessment and implications for conservation

Seed dispersal is one of the least understood phases in plant life-cycles, despite being recognized as fundamentally important for understanding species distribution, abundance, population dynamics and life-history variation. For species living in fragmented habitats, dispersal may be crucial for regional persistence. This paper synthesizes studies performed in Swedish semi-natural grasslands and deciduous forests. The main objective was to develop a simple method to assess the dispersal and colonization ability of plants. Dispersal and colonization were considered as a series of steps: seed production, seed transport and seedling recruitment. With the use of verified assumptions on (i) a trade-off between seed production and seed size, (ii) a relatively small predictive power of seed transport for species actual dispersal and colonization, (iii) a positive effect of seed size on recruitment, and (iv) a general prevalence of recruitment limitations by seed availability, a prediction is made that dispersal and colonization ability will be highest among species with intermediate seed sizes in a given community. This prediction is supported by field data. Based on estimated dispersal and colonization ability, and the ability of local populations to persist, a scheme is suggested with four basic categories of plants. Some implications are suggested for conservation, in a landscape scale, of plants belonging to each of these four categories.     

Efficiency of neural networks for prediction of in vitro culture conditions and inoculum properties for optimum productivity

This study represents an ANN based computational scheming of physical, chemical and biological parameters at flask level for mass multiplication of plants through micropropagation using bioreactors of larger volumes. The optimal culture environment at small scale for Glycyrrhiza plant was predicted by using neural network approach in terms of pH and volume of growth medium per culture flask, incubation room temperature and month of inoculation along with inoculum properties in terms of inoculum size, fresh weight and number of explant per flask. This kind of study could be a model system in commercial propagation of various economically important plants in bioreactors using tissue culture technique. In present course of study the ANN was trained by implementing MATLAB neural network. A feed-forward back propagation type network was created for input vector (seven input elements), with single hidden layer (seven nodes) and one output unit in output layer. The ‘tansig’ and ‘purelin’ transfer functions were adapted for hidden and output layers respectively. The four training functions viz. traingda, trainrp, traincgf, traincgb were randomly selected to train four networks which further examined with available dataset. The efficiency of neural networks was concluded by the comparison of results obtained from this study with that of empirical data obtained from the detailed tissue culture experiments and designated as Target set (mean fresh weight biomass per culture flask after 40 days of in vitro culture duration). Efficiency of networks for better training initialization was judged on the basis of comparative analysis of ‘Mean Square Error at zero epoch’ for each network trained in which the least error at initial point was observed with trainrp followed by traincgb and traincgf. A comparative assessment between experimental target data range obtained from wet lab practice and all trained network output range for the efficiency of trained networks for least deviation from target range revealed the output range of network ‘trainrp’ was closest to the empirical target range while least comparison was worked out from network ‘traincgb’ which had output range more than the target decided and ultimately showed meaningless result.     

Synthesis and evaluation of ethyleneoxylated and allyloxylated chalcone derivatives for imaging of amyloid β plaques by SPECT

We report radioiodinated chalcone derivatives as new SPECT imaging probes for amyloid β (Aβ) plaques. The monoethyleneoxy derivative 2 and allyloxy derivative 8 showed a high affinity for Aβ(1–42) aggregates with K_i values of 24 and 4.5 nM, respectively. Fluorescent imaging demonstrated that 2 and 8 clearly stained thioflavin-S positive Aβ plaques in the brain sections of Tg2576 transgenic mice. In vitro autoradiography revealed that [¹²⁵I]2 displayed no clear accumulation toward Aβ plaques in the brain sections of Tg2576 mice, whereas the accumulation pattern of [¹²⁵I]8 matched with the presence of Aβ plaques both in the brain sections of Tg2576 mice and an AD patient. In biodistribution studies using normal mice, [¹²⁵I]2 showed preferable in vivo pharmacokinetics (4.82%ID/g at 2 min and 0.45%ID/g at 60 min), while [¹²⁵I]8 showed only a modest brain uptake (1.62%ID/g at 2 min) with slow clearance (0.56%ID/g at 60 min). [¹²⁵I]8 showed prospective binding properties for Aβ plaques, although further structural modifications are needed to improve the blood brain barrier permeability and washout from brain.     

Production and characterization of mice transgenic for the A and B isoforms of human FcγRIII

Fcγ receptor (FcγR) engagement is pivotal for many effector functions of macrophages, polymorphonuclear neutrophils (PMN), and natural killer (NK) cells. Mice transgenic for the A and B isoforms of human (h) FcγRIII on macrophages, PMN, and NK cells were constructed to permit the study of mechanisms and potential in vivo strategies to utilize the cytotoxic effector and antigen-presenting functions of cells expressing the hFcγR. The present report characterizes the phenotypic and functional expression of hFcγRIII in transgenic mice derived by crossing hFcγRIIIA and hFcγRIIIB transgenic mice. Interleukin-2 (IL-2) induces hFcγRIII expression by myeloid cells and their precursors, and these transgenic receptors promote in vitro cytotoxicity and anti-hFcγRIII antibody internalization. Splenocytes from untreated and IL-2-treated hFcγRIIIA, hFcγRIIIB, and hFcγRIIIA/B mice exhibited enhanced in vitro cytotoxicity toward HER-2/neu-overexpressing SK-OV-3 human ovarian carcinoma cells when incubated with the murine bispecific mAb 2B1, which has specificity for HER-2/neu and hFcγRIII. These results indicate that hFcγRIII transgenes are expressed on relevant murine cellular subsets, exhibit inducible up-regulation patterns similar to those seen in humans, and code for functional proteins. hFcγRIII transgenic mice exhibiting specific cellular subset expression will permit the examination of strategies designed to enhance hFcγRIII-dependent immunological effector functions and will provide a model system in which to evaluate preclinically potential candidate molecules that recognize hFcγRIII for the immunotherapy of cancer. Received: 5 December 1998 / Accepted: 14 July 1999     

Clinical Efficacy and Tolerability of Praziquantel for Intestinal and Urinary Schistosomiasis—A Meta-analysis of Comparative and Non-comparative Clinical Trials

Background

Extensive use of praziquantel for treatment and control of schistosomiasis requires a comprehensive understanding of efficacy and safety of various doses for different Schistosoma species.

Methodology/Principal Findings

A systematic review and meta-analysis of comparative and non-comparative trials of praziquantel at any dose for any Schistosoma species assessed within two months post-treatment. Of 273 studies identified, 55 were eligible (19,499 subjects treated with praziquantel, control treatment or placebo). Most studied were in school-aged children (64%), S. mansoni (58%), and the 40 mg/kg dose (56%); 68% of subjects were in Africa. Efficacy was assessed as cure rate (CR, n = 17,017) and egg reduction rate (ERR, n = 13,007); safety as adverse events (AE) incidence. The WHO-recommended dose of praziquantel 40 mg/kg achieved CRs of 94.7% (95%CI 92.2–98.0) for S. japonicum, 77.1% (68.4–85.1) for S. haematobium, 76.7% (95%CI 71.9–81.2) for S. mansoni, and 63.5% (95%CI 48.2–77.0) for mixed S. haematobium/S. mansoni infections. Using a random-effect meta-analysis regression model, a dose-effect for CR was found up to 40 mg/kg for S. mansoni and 30 mg/kg for S. haematobium. The mean ERR was 95% for S. japonicum, 94.1% for S. haematobium, and 86.3% for S. mansoni. No significant relationship between dose and ERR was detected. Tolerability was assessed in 40 studies (12,435 subjects). On average, 56.9% (95%CI 47.4–67.9) of the subjects receiving praziquantel 40 mg/kg experienced an AE. The incidence of AEs ranged from 2.3% for urticaria to 31.1% for abdominal pain.

Conclusions/Significance

The large number of subjects allows generalizable conclusions despite the inherent limitations of aggregated-data meta-analyses. The choice of praziquantel dose of 40 mg/kg is justified as a reasonable compromise for all species and ages, although in a proportion of sites efficacy may be lower than expected and age effects could not be fully explored.     

Preparation and analysis of spermatocyte meiotic pachytene bivalents of pigs for gene mapping

Well-spread meiotic pachytene bivalents were obtained by using the prolonged hypotonic treatment com-bined with high chloroform Carnory’s fixative solution from cells of the testes of domestic pigs. Comparison in the division index and length of pachytene bivalents with metaphase chromosomes showed that those of the former are 5 times higher and 3.42(1.87-5.98) times longer than those of the latter. Comparative studies on chromomere maps of bivalents and mitotic chromosomal G-bands were conducted by using the chromo-some 12 as a example. Sex vesicle and various shapes of synaptic sex chromosomes have been observed.Two-color PRimed IN Situ (PRINS) labeling has been conducted successfully on pachytene bivalents of pigs.     

Screening strains for directed biosynthesis of β-d-mono-glucuronide-glycyrrhizin and kinetics of enzyme production

One fungus, tentatively named Penicillium sp. Li-3, was screened to biosynthesize β-d-mono-glucuronide-glycyrrhizin (GAMG), directly. Using glycyrrhizin as elicitor and the sole carbon source, this strain was capable of expressing β-d-glucuronidase, one intracellular enzyme with high substrate specificity. And glycyrrhizin was hydrolyzed directly into GAMG by enzyme from Penicillium sp. Li-3 with high production. It was found that the mol conversion ratio of this reaction was up to 88.45%. Research about kinetics of β-d-glucuronidase production showed that the cell growth and enzyme production of this strain was partial coupled. During the expressing of target enzyme, carbon catabolite repression existed, so only glycyrrhizin was the best carbon source as well as the elicitor. It was found that the surfactant (Tween 80 0.12%) could improve the ability of enzyme production markedly. Under the condition of initial pH 4.8 of the medium and 32 °C of the culture temperature, the maximum enzyme activity of 181.53 U ml⁻¹ was obtained.     

Neurofeedback—The Significance of Reinforcement and the Search for an Appropriate Strategy for the Success of Self-regulation

Nine healthy children took part in five sessions of feedback and instrumental conditioning of slow cortical potentials (SCPs). The feedback conditions (the relation between the feedback signal and amplitude of SCP) were inverted after two sessions. Neither the children nor the therapists were aware of this change. The adjustment of the children to the new feedback setting and the self-regulation strategies employed were investigated. The results were as follows: (a) Healthy children achieved control over cortical negativity within two sessions. (b) The change of feedback conditions worsened the regulation abilities, which then improved again within the following three sessions. (c) After the first two sessions, the participants were able to describe strategies that were successful during different phases of self-regulation. (d) Following the change in the feedback conditions, the children re-evaluated the way they influenced their SCPs. However, they did not alter the cognitive or behavioral strategies. The study demonstrated that positive and negative reinforcement and the knowledge of results are more important for successful self-regulation than the search for effective strategies. The relevance of these findings is discussed.