ABSTRACT
Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.
Subject(s)
Domestication , Genetic Variation , Genome, Plant , Genome-Wide Association Study , Genomics , Oryza/genetics , Quantitative Trait, Heritable , RNA, Untranslated , Crops, Agricultural , Edible Grain , Evolution, Molecular , Gene Expression Profiling , Gene Expression Regulation, Plant , Genomics/methods , PhenotypeABSTRACT
In this paper, a shear force scanning near-field fluorescence microscope combined with a confocal laser microspectrofluorometer is described. The shear force detection is realized based on a bimorph cantilever, which provides a very sensitive, reliable, and easy to use method to control the probe-sample distance during scanning. With the system, high-quality shear force imaging of various samples has been carried out. Furthermore, simultaneous shear force and near-field fluorescence imaging of biological cells has also been realized. As an example, we especially present the result on the distribution of P-glycoprotein in the plasma membrane of human small cell lung cancer cells, suggesting that the system would be a promising tool for biological applications.
Subject(s)
ATP Binding Cassette Transporter, Subfamily B/metabolism , Carcinoma, Small Cell/ultrastructure , Lung Neoplasms/ultrastructure , Microscopy, Electron, Scanning/instrumentation , Microscopy, Electron, Scanning/methods , Carcinoma, Small Cell/metabolism , Cell Line, Tumor , Humans , Lung Neoplasms/metabolism , Microscopy, Confocal/instrumentation , Microscopy, Confocal/methodsABSTRACT
A non-optical bimorph-based tapping-mode force sensing method for tip-sample distance control in scanning near-field optical microscopy is developed. Tapping-mode force sensing is accomplished by use of a suitable piezoelectric bimorph cantilever, attaching an optical fibre tip to the extremity of the cantilever free end and fixing the guiding portion of the fibre to a stationary part near the tip to decouple it from the cantilever. This method is mainly characterized by the use of a bimorph, which carries out simultaneous excitation and detection of mechanical vibration at its resonance frequency owing to piezoelectric and anti-piezoelectric effects, resulting in simplicity, compactness, ease of implementation and lack of parasitic optical background. In conjugation with a commercially available SPM controller, tapping-mode images of various samples, such as gratings, human breast adenocarcinoma cells, red blood cells and a close-packed layer of 220-nm polystyrene spheres, have been obtained. Furthermore, topographic and near-field optical images of a layer of polystyrene spheres have also been taken simultaneously. The results suggest that the tapping-mode set-up described here is reliable and sensitive, and shows promise for biological applications.
Subject(s)
Erythrocytes/ultrastructure , Humans , Microscopy, Electron, Scanning/methods , VibrationABSTRACT
BACKGROUND: Twelve genetic types of autosomal dominant hereditary ataxia have been recently identified and the genes responsible for most of them cloned. Molecular identification of the type of ataxia is important to determine the disease prevalence and its natural history in various populations. OBJECTIVES: To perform molecular analysis of 75 Chinese families affected with spinocerebellar ataxia (SCA) and to evaluate the spectrum of mutations in these genes and the correlation between genotypes and phenotypes in Chinese patients. SETTING: Neurogenetics Unit, China-Japan Friendship Hospital, Beijing, China. METHODS: One hundred nine patients from 75 kindreds diagnosed as having autosomal dominant SCA, 16 patients with sporadic SCA or spastic paraplegia, 280 control chromosomes of the Chinese population, and 120 control chromosomes of the Sakha population were selected for this study. We conducted detailed mutational analysis by direct sequencing of polymerase chain reaction products amplified from genomic DNA. RESULTS: Spinocerebellar ataxia type 1 (SCA1) was identified in 5 families with 12 studied patients. All affected family members were heterozygous for a CAG repeat expansion in the SCA1 gene containing 51 to 64 trinucleotide repeats. Normal alleles had 26 to 35 repeats. Spinocerebellar ataxia type 1 accounted for 7% of the studied Chinese families with ataxia. In addition, we determined the frequency of a single vs double CAT interruption in 120 control chromosomes of the Siberian Sakha population, which has the highest known prevalence of SCA1, and compared this with 280 control chromosomes from the Chinese populations. The results show that 64.7% of the Siberian normal alleles contain a single CAT interruption, whereas 92% of the Chinese had more than 1 interruption. CONCLUSIONS: Spinocerebellar ataxia type 1 is responsible for 7% of affected families in the Chinese population. A correlation between the prevalence of SCA1 and the number of CAT interruptions in the trinucleotide chain suggests that a CAT-to-CAG substitution may have been the initial event contributing to the generation of expanded alleles and influencing relative prevalence of SCA1.
Subject(s)
Asian People/genetics , Spinocerebellar Ataxias/genetics , Adult , Alleles , Ataxia/classification , Ataxia/genetics , Ataxin-1 , Ataxins , Base Sequence/genetics , China , Chromosome Mapping , Ethnicity/genetics , Female , Gene Frequency , Genotype , Heterozygote , Humans , Male , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , Phenotype , Reference Values , Siberia , Spinocerebellar Ataxias/physiopathology , Trinucleotide RepeatsABSTRACT
Gel chromatography was employed to measure relative molecular mass distribution of lignin dispersants. The results show that relative molecular mass distribution of Reax-85A(I) and M-9(II) are respectively to be from 500 to 35,000 and from 1,000 to 50,000. The fractions separated from (I) and (II) by thin layer chromatography were also investigated through gel chromatography to prove that these fractions were mainly separated depending on relative molecular mass.
