Gene expression variability within and between human populations and implications toward disease susceptibility

Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals.

Many human genes have population-specific expression levels, which are linked to population-specific polymorphisms and copy-number variations. However, it is unclear whether human genes show similar dynamic range of expression between populations. In this work we analyzed HapMap gene expression compendium, and quantified the between-population and within-population expression variability for ∼18,000 human transcripts. We first concluded that the majority of the human genes have similar levels of within-population variability. However, a small fraction (∼4%) does show much higher expression variability in one population, and the deviation is consistently associated with increased SNP heterozygosity in their UTR regulatory regions. We further showed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling associated with HIV-1 infection. Combined with the finding that human HIV-1 host factors tend to have increased expression variability within populations, our analysis may explain, at least in part, different susceptibility to HIV infection within the human population. This work provides a fresh angle for analyzing gene expression variations in populations.

Development of functional nanoprobes for optical near-field characterization

Subwavelength optical imaging can be accomplished by scanning a nanoscale aperture or a nanoprobe containing a locally defined nanoscale optical source. Currently, most such methods, including various implementations of near-field scanning optical microscopy (NSOM), form near-field images by measuring the intensity of optical signals generated by optical transmission, scattering or fluorescence. Here we report the development of a nanoprobe that can extend NSOM functionalities by focusing on the dynamical aspects of light emission (such as fluorescence lifetime measurement) and nonlinear optical processes (such as second harmonic generation). Our nanoprobes consist of a silica fiber taper, a single nanowire or a nanotube, and appropriate functional nano-optical structures. The fabrication, characterization and potential applications of such nanoprobes are discussed.

Maternal and fetal tissue accumulation of selected endocrine disrupting compounds (EDCs) following exposure to sewage sludge-treated pastures before or after conception

Liver concentrations of selected pollutant classes were determined in groups of sheep fetuses and their dams, at 55 (Experiment 1) and 110 (Experiment 2) days of gestation (term = 145 d) following exposure, throughout their breeding lives and after mating, to pasture treated with either inorganic fertiliser (control, CC) or with sewage sludge (treated, TT). In a unique study designed to separate the respective contributions of environmental sources and mobilised tissue to the available EDC burden, in additional groups of animals, pollutant burdens at 110 days gestation were assessed following exposure to the respective treatments, either throughout their breeding lives until mating, but not thereafter (TC), or only between mating and slaughter (CT) (Experiment 3). With very few exceptions, maternal and fetal liver concentrations of diethylhexyl phthalate (DEHP) and selected polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDE) and polycyclic aromatic hydrocarbons (PAHs) were not significantly affected by sludge exposure in any group. In some cases, maternal and fetal tissue EDC concentrations were different but the differences were not consistent, and maternal and fetal concentrations of none of the classes of chemical were significantly correlated. It was not possible to identify a single chemical, or class of chemical, that may be responsible for previously observed physiological effects of exposure to sludge-treated pastures. It is concluded that exposure of sheep to pastures fertilised with sewage sludge was not associated with increased liver concentrations of EDCs, irrespective of the stage of development at which they were measured and of maternal tissue mobilisation and EDC release during gestation. Thus, retrospective measurements of EDC tissue burdens could not be used to accurately assess earlier fetal EDC insults.

First measurement of Bose-Einstein correlations in proton-proton collisions at √s=0.9 and 2.36 TeV at the LHC

Bose-Einstein correlations have been measured using samples of proton-proton collisions at 0.9 and 2.36 TeV center-of-mass energies, recorded by the CMS experiment at the CERN Large Hadron Collider. The signal is observed in the form of an enhancement of pairs of same-sign charged particles with small relative four-momentum. The size of the correlated particle emission region is seen to increase significantly with the particle multiplicity of the event.

Angiotensin-converting enzyme insertion/deletion polymorphism associated with acute respiratory distress syndrome among caucasians

Studies investigating the association between angiotensin-converting enzyme (ACE) insertion/deletion polymorphisms and the risk of acute respiratory distress syndrome (ARDS) report conflicting results. The objective of the present study was to summarize quantitatively the evidence for such a relationship. Two investigators independently searched the MEDLINE (January 1966 - October 2009) and EMBASE (January 1980 - October 2009) databases. This meta-analysis included six case-control studies, which included 514 ARDS cases and 2619 controls. The combined results based on all studies showed that patients with ARDS had a significantly higher frequency of the ACE deletion/deletion (DD) genotype (odds ratio [OR] 1.56; 95% confidence interval [CI] 1.22, 2.00) than controls. When stratifying for race, no significant differences in genotype distribution were found except that Caucasian patients with ARDS had a significantly higher frequency of the DD genotype (OR 1.65; 95% CI 1.27, 2.13) than controls. This meta-analysis suggests that ACE insertion/deletion polymorphisms may be associated with ARDS among Caucasians.

Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV

Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.

High-content analysis in monastrol suppressor screens. A neural network-based classification approach

OBJECTIVES

High-content screening (HCS) via automated fluorescent microscopy is a powerful technology for the effective expression of cellular processes. However, HCS will generally produce tremendous image datasets, which leads to difficulties of handling and analyzing. We proposed an automatic classification approach for simultaneous feature extraction and cell phenotype recognition of monoaster and bipolar cells in HCS system.

METHODS

The proposed approach was composed of image segmentation, feature extraction, and classification. The image segmentation was based on the Laplacian of Gaussian (LoG) edge detection method. For the reduction of noise effect on cellular images, we employed an adaptive threshold in microtubule channel. The principal component analysis was used in the feature selection process. The classification was performed with a back-propagation neural network (BPNN). Using the current approach, the cell phases were distinguished from three-channel acquisitions of cellular images and the numbers of bipolar and monoaster cells were automatically counted.

RESULTS

The validity of this approach was examined by the application of screening the response of drug compounds in suppressing Monastrol. Our results indicate that the proposed algorithm could improve the recognition rates of monoaster and bipolar cells to 97.98% and 93.12%, respectively, compared with 97.02% and 86.96% obtained from the same samples by multi-phenotypic mitotic analysis (MMA).

CONCLUSIONS

We have shown that BPNN is a valuable tool to classify cell phenotype. To further improve the classification performance, more test data, more optimized feature selection approaches, and advanced classifier may be required and will be investigated in future works.

A novel endophytic Huperzine A-producing fungus, Shiraia sp. Slf14, isolated from Huperzia serrata

AIMS

To characterize and identify a novel Huperzine A (HupA)-producing fungal strain Slf14 isolated from Huperzia serrata (Thunb. ex Murray) Trev. in China.

METHODS AND RESULTS

The isolation, identification and characterization of a novel endophytic fungus producing HupA specifically and consistently from the leaves of H. serrata were investigated. The fungus was identified as Shiraia sp. Slf14 by molecular and morphological methods. The HupA produced by this endophytic fungus was shown to be identical to authentic HupA analysed by thin layer chromatographic, High-performance liquid chromatography (HPLC), LC-MS, (1) H NMR and acetylcholinesterase (AChE) inhibition activity in vitro. The amount of HupA produced by Shiraia sp. Slf14 was quantified to be 327.8 μg l(-1) by HPLC, which was far higher than that of the reported endophytic fungi, Acremonium sp., Blastomyces sp. and Botrytis sp.

CONCLUSIONS

The production of HupA by endophyte Shiraia sp. Slf14 is an enigmatic observation. It would be interesting to further study the HupA production and regulation by the cultured endophyte in H. serrata and in axenic cultures.

SIGNIFICANCE AND IMPACT OF THE STUDY

Although the current accumulation of HupA by the endophyte is not very high, it could provide a promising alterative approach for large-scale production of HupA. However, further strain improvement and the fermentation process optimization are required to result in the consistent and dependable production.

Epitaxial growth and the art of computer simulations

The results of kinetic simulations of the aggregates formed during the deposition of atoms on a semiconductor surface are reviewed. Because the kinetic parameters are poorly known and the accuracy of the existing interatomic potentials has not been sufficiently tested, the goal has been to reach a qualitative understanding of the formation of unusual patterns during growth, such as the segregation of aluminum during the growth of aluminum-gallium-arsenide (AlGaAs) coherent tilted superlattices and the formation of thin, long, and parallel islands during the deposition of Si on an Si(100) surface. Kinetic mechanisms for these phenomena are proposed.

First Report of Alternaria Leaf Blight on Bupleurum chinense Caused by Alternaria alternata in China

Bupleurum chinense DC. (family Umbelliferae) is an important medicinal herb in traditional Chinese medicine and is cultivated as an economically important plant in China (2). From 2006 to 2009, severe foliar disease was observed on B. chinense in Haidian, Changping, and Shunyi districts, Beijing, China. Approximately 75 to 85% of fields were affected with disease incidence ranging from 65 to 90%. Distribution of the disease in affected B. chinense fields was generally associated with high soil moisture, often corresponding to poor drainage. Initial symptoms first appeared on older leaves as irregularly shaped, minute, dark brown-to-black spots, with yellow borders on the edge of the affected leaflet blade. As the disease progressed, the lesions expanded, causing the leaflets to turn brown, shrivel, and die. Isolations performed on potato dextrose agar (PDA) initially resulted in white colonies. After 7 days of incubation at 25°C, the colonies turned gray or brown. Conidia varied in size from 10 × 6 to 40 × 12 μm, appeared brown to dark brown or olive-brown, were short beaked and borne in long chains, oval and bean-shaped with one to six transverse septa and zero to three longitudinal septa. Sequences of the rDNA from the internal transcribed spacer regions 1 and 2 and the 5.8S gene were amplified using primers ITS1 and ITS4, were obtained from three isolates, and comparisons with GenBank showed 100% similarity with A. alternata (Genbank Accession No. AB470912.1). For pathogenicity tests, three isolates were grown on PDA for 14 days. Inoculations were performed on detached, surface-sterilized, and healthy B. chinense leaflets following the method of Belisario (1). A 5-μl drop of conidial suspension containing 1 × 10⁵ CFU/ml was placed on each leaflet and 12 leaves per isolate were used. Leaves were incubated in a growth chamber (80 to 90% relative humidity; 50 to 60 klx/m² light intensity with a 12-h photoperiod). After 5 days, leaf spots similar to the original symptoms developed on all inoculated leaves and A. alternata was consistently reisolated from symptomatic leaf tissues on PDA. Control leaflets inoculated with sterile water remained asymptomatic. The experiment was performed three times. To our knowledge, this is the first report of A. alternata on B. chinense from China. References: (1) A. Belisario et al. Plant Dis. 83:696, 1999. (2) C. Sui et al. Plant Dis. 93:844, 2009.

Ultrathin single-crystal ZnO nanobelts: Ag-catalyzed growth and field emission property

We report the growth of ultrathin single-crystal ZnO nanobelts by using a Ag-catalyzed vapor transport method. Extensive transmission electron microscopy and atomic force microscopy measurements reveal that the thickness of the ultrathin ZnO nanobelts is approximately 2 nm. Scanning electron microscopy and post-growth annealing studies suggest a '1D branching and 2D filling' growth process. Our results demonstrate the critical role of catalyst in the deterministic synthesis of nanomaterials with the desired morphology. In addition, these ultrafine nanobelts exhibit stable field emission with unprecedented high emission current density of 40.17 mA cm(-2). These bottom-up building blocks of ultrathin ZnO nanobelts may facilitate the construction of advanced electronic and photonic nanodevices.

Karyotyping in melon (Cucumis melo L.) by cross-species fosmid fluorescence in situ hybridization

Chromosome identification is critical for cytogenetic research and will accelerate studies on genetic variation and breeding, especially for those species with relatively little sequence information. So far, no reliable cytological landmarks have been developed to distinguish individual chromosomes in melon. In this study, using FISH (fluorescence in situ hybridization) combined with comparative genome information, we selected 21 cucumber fosmids anchored by SSR markers as chromosome-specific cytological markers for melon chromosomes. Moreover, with the help of melon centromeric satellite DNA repeats CentM, 45S rDNA and 5S rDNA, sequential FISH with 3 sets of multi-fosmid cocktails were conducted on the same metaphase cell, which allowed us to simultaneously identify each of the 12 metaphase chromosomes of melon and a standardized melon karyotype of somatic metaphase chromosomes was constructed. Finally, we compared the distribution of 21 FISH-mapped fosmids between melon and cucumber chromosomes, which allows a better understanding of the evolutionary process shaping these 2 species. Our study provides a basis for cytological characterization of the melon genome and comparative genomics of Cucurbitaceae.

Estimation of disruption of animal cells by laminar shear stress

Using mechanical cell properties measured by micromanipulation, and a model of cell distortion in laminar flow fields, a method has been developed for predicting disruption of animal cells by laminar shear stresses. Predictions of the model were compared with measured losses of cell number and viability of TB/C3 murine hybridomas sheared in a cone and plate viscometer at shear rates up to 3950 s(-1), and shear stresses up to 600 Nm(-2), achieved by enhancement of viscosity with dextran. In all cases, the experimental, results and predictions were within 30%. Such excellent agreement suggests it might be possible to use micromanipulation measurements of animal cell mechanical properties to predict cell damage in more complex flow fields, such as those in bioreactors.

Peroxisome proliferator-activated receptor-gamma(PPARgamma) agonist improves coronary artery endothelial function in diabetic patients with coronary artery disease

The aim of this study was to assess the effect of rosiglitazone on endothelial function of the coronary arteries and on plasma levels of inflammatory markers in diabetic patients with coronary artery disease (CAD). Fifty-six patients with type 2 diabetes and CAD were randomized to receive either rosiglitazone (4 mg/day) or a control for 12 weeks. The coronary flow velocity reserve (CFVR) was assessed using transthoracic Doppler echocardiography at baseline and after 12 weeks. After 12 weeks of rosiglitazone treatment, plasma levels of C-reactive protein were significantly decreased and the median CFVR was significantly increased compared with baseline levels and compared with the control group. These results suggest that, in addition to its beneficial metabolic effects, rosiglitazone, via its anti-inflammatory effects, may improve endothelial function of the coronary arteries in patients with diabetes and CAD.

Quick and effective technique for specimen extraction during video-assisted thoracic surgery

We describe here a novel technique for specimen extraction during video-assisted thoracic surgery. Traditionally, most surgeons extract specimens using a tough nylon sac or bag. However, this procedure is time-consuming and difficult for trainees to perform. We developed a novel extraction sac with two positioning finger sacs. Our technique consists of first grasping the specimen and then enclosing it with the sac instead of placing the specimen into the sac. By grasping the specimen and performing a movement resembling the drawing off of a glove, the resected specimen is inserted into the bag and can be subsequently extracted. We conclude that this new strategy is an effective, quick and safe technique.

Oxytocin and vasopressin immunoreactive staining in the brains of Brandt's voles (Lasiopodomys brandtii) and greater long-tailed hamsters (Tscherskia triton)

Immunoreactive (ir) staining of the neuropeptides oxytocin (OT) and vasopressin (AVP) was performed in the brains of Brandt's voles (Lasiopodomys brandtii) and greater long-tailed hamsters (Tscherskia triton)-two species that differ remarkably in social behaviors. Social Brandt's voles had higher densities of OT-ir cells in the medial preoptic area (MPOA) and medial amygdala (MeA) as well as higher densities of AVP-ir cells in the lateral hypothalamus (LH) compared to solitary greater long-tailed hamsters. In contrast, the hamsters had higher densities of OT-ir cells in the anterior hypothalamus (AH) and LH and higher densities of AVP-ir cells in the MPOA than the voles. OT-ir and AVP-ir fibers were also found in many forebrain areas with subtle species differences. Given the roles of OT and AVP in the regulation of social behaviors in other rodent species, our data support the hypothesis that species-specific patterns of central OT and AVP pathways may underlie species differences in social behaviors. However, despite a higher density of OT-ir cells in the paraventricular nucleus of the hypothalamus (PVN) in females than in males in both species, no other sex differences were found in OT-ir or AVP-ir staining. These data failed to support our prediction that a sexually dimorphic pattern of neuropeptide staining in the brain is more apparent in Brandt's voles than in greater long-tailed hamsters.

In vivo degradation of calcium phosphate cement incorporated into biodegradable microspheres

In this study we have investigated the influence of the mechanism of microsphere degradation or erosion on the in vivo degradation of microsphere/calcium phosphate cement composites (microsphere CPCs) used in tissue engineering. Microspheres composed of poly(lactic-co-glycolic acid) (PLGA), gelatin and poly(trimethylene carbonate) (PTMC) were used as the model and the resulting microsphere CPCs were implanted subcutaneously for 4, 8 or 12weeks in the back of New Zealand white rabbits. Besides degradation, the soft tissue response to these formulations was evaluated. After retrieval, specimens were analyzed by physicochemical characterization and histological analysis. The results showed that all microsphere CPCs exhibited microsphere degradation after 12weeks of subcutaneous implantation, which was accompanied by decreasing compression strength. The PLGA microspheres exhibited bulk erosion simultaneously throughout the whole composite, whereas the gelatin type B microspheres were degradated from the outside to the center of the composite. High molecular weight PTMC microspheres exhibited surface erosion resulting in decreasing microsphere size. Furthermore, all composites showed a similar tissue response, with decreasing capsule thickness over time and a persistent moderate inflammatory response at the implant interface. In conclusion, microsphere CPCs can be used to generate porous scaffolds in an in vivo environment after degradation of microspheres by various degradation/erosion mechanisms.

Protein production using recombinant yeast in an immobilized-cell-film airlift bioreactor

A recombinant Saccharomyces cerevisiae C468/pGAC9 (ATCC 20690), which expresses Aspergillus awamori glucoamylase gene under the control of the yeast enolase I (ENO1) promoter and secretes glucoamylase into the extracellular medium, was used as a model system to investigate the effect of cell immobilization on bioreactor culture performance. Free suspension cultures in stirred-tank and airlift bioreactors confirmed inherent genetic instability of the recombinant yeast. An immobilized-cell-film airlift bioreactor was developed by employing cotton cloth sheets to immobilize the yeast cells by attachment. Enhanced enzyme productivity and production stability in the immobilized-cell system were observed. Experimental data indicated that the immobilized cells maintained a higher proportion of plasmid-bearing cells for longer periods under continuous operation. The higher plasmid maintenance with immobilized cells is possibly due to reduced specific growth rate and increased plasmid copy number. Double-selection pressure was used to select and maintain the recombinant yeast. The selected strain showed better production performance than the original strain. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 241-251, 1997.