Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed

A genome-based study of the Muslim Hui community and the Han population of Liaoning province, PR China

To investigate the proposed historical origins of the Hui, a Chinese Muslim minority resident in Liaoning Province, PR China, DNA samples obtained from 53 individuals were analyzed at ten autosomal and six Y-chromosome microsatellite loci. As reference sources, equivalent samples were investigated from the coresident Han majority population. Both the Hui and the Han exhibited appreciable genetic heterogeneity in terms of the size, number, and size range of alleles, suggestive of population substructure resulting from their particular cultural and historical backgrounds. The contrast in the patterns of autosomal and Y-chromosome diversity of the two communities was obvious. Analysis of molecular variance showed that only 4.6% of total autosomal molecular variance was due to differences between the Hui and Han. The comparable value for Y-chromosome haplotype distributions of 14.0% indicated that the Hui and Han of Liaoning have separate paternal genetic histories

Optimal quantum pump in the presence of a superconducting lead

We investigate the parametric pumping of a hybrid structure consisting of a normal quantum dot, a normal lead and a superconducting lead. Using the time dependent scattering matrix theory, we have derived a general expression for the pumped electric current and heat current. We have also derived the relationship among the instantaneous pumped heat current, electric current, and shot noise. This gives a lower bound for the pumped heat current in the hybrid system similar to that of the normal case obtained by Avron et al

Enterococcus faecalis from healthy infants modulates inflammation through MAPK signaling pathways

10.1371/journal.pone.0097523PLoS ONE95-POLN

Observed photodetachment in parallel electric and magnetic fields

We investigate photodetachment from negative ions in a homogeneous 1.0-T magnetic field and a parallel electric field of approximately 10 V/cm. A theoretical model for detachment in combined fields is presented. Calculations show that a field of 10 V/cm or more should considerably diminish the Landau structure in the detachment cross section. The ions are produced and stored in a Penning ion trap and illuminated by a single-mode dye laser. We present preliminary results for detachment from S- showing qualitative agreement with the model. Future directions of the work are also discussed.Comment: Nine pages, five figures, minor revisions showing final publicatio

Nature of Correlated Motion of Electrons in the Parent Cobaltate Superconductors

Recently discovered class of cobaltate superconductors (Na0.3CoO2.nH2O) is a novel realization of interacting quantum electron systems in a triangular network with low-energy degrees of freedom. We employ angle-resolved photoemission spectroscopy to uncover the nature of microscopic electron motion in the parent superconductors for the first time. Results reveal a large hole-like Fermi surface (consistent with Luttinger theorem) generated by the crossing of super-heavy quasiparticles. The measured quasiparticle parameters collectively suggest a two orders of magnitude departure from the conventional Bardeen-Cooper-Schrieffer electron dynamics paradigm and unveils cobaltates as a rather hidden class of relatively high temperature superconductors.Comment: 5 pages, 4 figures, 1 tabl

Modelling and Interpreting The Effects of Spatial Resolution on Solar Magnetic Field Maps

Different methods for simulating the effects of spatial resolution on magnetic field maps are compared, including those commonly used for inter-instrument comparisons. The investigation first uses synthetic data, and the results are confirmed with {\it Hinode}/SpectroPolarimeter data. Four methods are examined, one which manipulates the Stokes spectra to simulate spatial-resolution degradation, and three "post-facto" methods where the magnetic field maps are manipulated directly. Throughout, statistical comparisons of the degraded maps with the originals serve to quantify the outcomes. Overall, we find that areas with inferred magnetic fill fractions close to unity may be insensitive to optical spatial resolution; areas of sub-unity fill fractions are very sensitive. Trends with worsening spatial resolution can include increased average field strength, lower total flux, and a field vector oriented closer to the line of sight. Further-derived quantities such as vertical current density show variations even in areas of high average magnetic fill-fraction. In short, unresolved maps fail to represent the distribution of the underlying unresolved fields, and the "post-facto" methods generally do not reproduce the effects of a smaller telescope aperture. It is argued that selecting a method in order to reconcile disparate spatial resolution effects should depend on the goal, as one method may better preserve the field distribution, while another can reproduce spatial resolution degradation. The results presented should help direct future inter-instrument comparisons.Comment: Accepted for publication in Solar Physics. The final publication (including full-resolution figures) will be available at http://www.springerlink.co

STM characterization of the Si-P heterodimer

We use scanning tunneling microscopy (STM) and Auger electron spectroscopy to study the behavior of adsorbed phosphine (PH$_{3}$) on Si(001), as a function of annealing temperature, paying particular attention to the formation of the Si-P heterodimer. Dosing the Si(001) surface with ${\sim}$0.002 Langmuirs of PH$_{3}$ results in the adsorption of PH$_{x}$ (x=2,3) onto the surface and some etching of Si to form individual Si ad-dimers. Annealing to 350$^{\circ}$C results in the incorporation of P into the surface layer to form Si-P heterodimers and the formation of short 1-dimensional Si dimer chains and monohydrides. In filled state STM images, isolated Si-P heterodimers appear as zig-zag features on the surface due to the static dimer buckling induced by the heterodimer. In the presence of a moderate coverage of monohydrides this static buckling is lifted, rending the Si-P heterodimers invisible in filled state images. However, we find that we can image the heterodimer at all H coverages using empty state imaging. The ability to identify single P atoms incorporated into Si(001) will be invaluable in the development of nanoscale electronic devices based on controlled atomic-scale doping of Si.Comment: 6 pages, 4 figures (only 72dpi

Paclitaxel-octreotide conjugates inhibit growth of human non-small cell lung cancer cells in vitro

Aim: To evaluate the effects of paclitaxel-octreotide conjugates on the growth of cultured non-small cell lung cancer cells. Methods: RT-PCR was performed to detect mRNA for the subtypes of the human somatostatin receptor (SSTR) using specific primers. MTT-based cytotoxicity assay was used to evaluate the cell viability after treatment with paclitaxel and the conjugates. Cell cycle perturbations were determined using a Fluorescence-Activated Cell Sorter. Results: Non-small cell lung cancer A549 and Calu-6 cells expressed mRNA for SSTR2 and SSTR5. Paclitaxel and the conjugates effectively inhibited the growth of A549 and Calu-6 cells in a concentration- and time-dependent manner. In SSTR-negative fibroblasts, the conjugates were less cytotoxic than paclitaxel. The conjugates and paclitaxel could induce the increase of G2/M phase ratio in A549 cells. Conclusion: The paclitaxel-octreotide conjugates can be used as selective-targeted chemotherapeutic agents for treating non-small cell lung cancer.Цель: оценить эффект конъюгатов паклитаксела-октреотида на рост культивированных клеток немелкоклеточного рака легкого человека. Методы: для определения мРНК подтипов рецептора соматостатина человека (SSTR) применяли ОT-ПЦР. Анализ цитотоксичности в МТТ-тесте применяли для оценки выживаемости клеток после их инкубации с паклитакселом и конъюгатами. Нарушения клеточного цикла определяли с применением FACS — клеточного сортера. Результаты: установлено, что клеточные линии немелкоклеточного рака легкого A549 и Calu-6 экспрессируют SSTR2 и SSTR5 мРНК. Отмечено эффективное дозо- и времязависимое угнетение роста клеток A549 и Calu-6 паклитакселом и конъюгатами. Для SSTR-негативных фибробластов конъюгаты менее цитотоксичны, чем паклитаксел. Конъюгаты и паклитаксел могут индуцировать повышение соотношения фаз G2 /M в клетках A549. Выводы: конъюгаты паклитаксел-октреотида могут быть использованы как селективные химиотерапевтические агенты для воздействия на немелкоклеточный рак легкого