Extensive Phenotypic Variation in Early Flowering Mutants of Arabidopsis

Flowering time, the major regulatory transition of plant sequential development, is modulated by multiple endogenous and environmental factors. By phenotypic profiling of 80 early flowering mutants of Arabidopsis, we examine how mutational reduction of floral repression is associated with changes in phenotypic plasticity and stability. Flowering time measurements in mutants reveal deviations from the linear relationship between the number of leaves and number of days to bolting described for natural accessions and late flowering mutants. The deviations correspond to relative early bolting and relative late bolting phenotypes. Only a minority of mutants presents no detectable phenotypic variation. Mutants are characterized by a broad release of morphological pleiotropy under short days, with leaf characters being most variable. They also exhibit changes in phenotypic plasticity across environments for florigenic-related responses, including the reaction to light and dark, photoperiodic behavior, and Suc sensitivity. Morphological pleiotropy and plasticity modifications are differentially distributed among mutants, resulting in a large diversity of multiple phenotypic changes. The pleiotropic effects observed may indicate that floral repression defects are linked to global developmental perturbations. This first, to our knowledge, extensive characterization of phenotypic variation in early flowering mutants correlates with the reports that most factors recruited in floral repression at the molecular genetic level correspond to ubiquitous regulators. We discuss the importance of functional ubiquity for floral repression with respect to robustness and flexibility of network biological systems

Evidence for Chromatin-Remodeling Complex PBAP-Controlled Maintenance of the <i>Drosophila</i> Ovarian Germline Stem Cells

<div><p>In the <i>Drosophila</i> oogenesis, germline stem cells (GSCs) continuously self-renew and differentiate into daughter cells for consecutive germline lineage commitment. This developmental process has become an <i>in vivo</i> working platform for studying adult stem cell fate regulation. An increasing number of studies have shown that while concerted actions of extrinsic signals from the niche and intrinsic regulatory machineries control GSC self-renewal and germline differentiation, epigenetic regulation is implicated in the process. Here, we report that Brahma (Brm), the ATPase subunit of the <i>Drosophila</i> SWI/SNF chromatin-remodeling complexes, is required for maintaining GSC fate. Removal or knockdown of Brm function in either germline or niche cells causes a GSC loss, but does not disrupt normal germline differentiation within the germarium evidenced at the molecular and morphological levels. There are two <i>Drosophila</i> SWI/SNF complexes: the Brm-associated protein (BAP) complex and the polybromo-containing BAP (PBAP) complex. More genetic studies reveal that mutations in <i>polybromo</i>/<i>bap180</i>, rather than gene encoding Osa, the BAP complex-specific subunit, elicit a defect in GSC maintenance reminiscent of the <i>brm</i> mutant phenotype. Further genetic interaction test suggests a functional association between <i>brm</i> and <i>polybromo</i> in controlling GSC self-renewal. Taken together, studies in this paper provide the first demonstration that Brm in the form of the PBAP complex functions in the GSC fate regulation.</p></div

<i>brm</i> genetically interacts with <i>bap180</i> but not <i>osa</i> in maintaining GSCs.

<p>*<i>p</i><0.05.</p

<i>osa</i> mutations do not disrupt GSC maintenance in the ovary.

<p><i>osa</i> mutations do not disrupt GSC maintenance in the ovary.</p

Removal or knock down of <i>brm</i> or <i>bap180</i> function does not disrupt germline differentiation within the germarium.

<p>(A–J′) Germaria containing <i>brm^T362</i> (A–E′) or <i>bap180^Δ86</i> (F–J′) mutant germ cell clones (broken circles) marked by the absence of nuclear GFP, stained for Sxl (A, A′, F, F′), A2BP1 (B, B′, G, G′), Nanos (C, C′, H, H′), Bruno (D, D′, I, I′) or Orb (E, E′, J, J′). GSC-derived germline differentiation within the germarium proceeds with dynamic expression of a number of molecular markers such as Sxl in GSCs/CBs (A, A′, F, F′), A2BP1 in germ cells starting from the 4-cell cysts (B, B′, G, G′), Nanos in 16-cell germline cysts (C, C′, H, H′), Bruno in germ cells of the 16-cell cysts (D, D′, I, I′) and Orb in oocyte of the 16-cell cysts (E, E′, J, J′). The expression pattern of all tested differentiation markers remains unchanged in the germline clones homozygous for either <i>brm^T362</i> (A–E′) or <i>bap180^Δ86</i> (F–J′). (K) Graph shows that compared with the controls, <i>brm</i> knockdown in ECs does not cause the accumulation of UGCs in the germarium over a 14-day time course after eclosion.</p

Mutation or reduced expression of <i>brm</i> or <i>polybromo/bap180</i> in the germline causes a defective GSC maintenance.

<p>(A, A′) In the wild type germarium, <i>brm</i> is ubiquitously expressed in almost all cell types, predominantly in TFs, CpCs, ECs and follicle cells (FCs). (B–I) Germaria with the control (B, C, F, G) or <i>brm^T362</i> (D, E) or <i>bap180^Δ86</i> (H, I) mutant GSC clones (broken circles) marked by the absence of GFP and the presence of an anteriorly anchored spectrosome (α-spectrin staining). In the wild type controls, marked GSCs are evident at 2 days and 14 days ACI (B, C, F, G). Conversely, marked GSCs mutant for <i>brm</i> (D) or <i>bap180</i> (H) are only detected at 2 days ACI, but lost at 14 days ACI (E, I). Instead, the mutant cyst clones are present in the germaria (arrows in E and I). (J, K) The control (J) and <i>brm</i> knockdown (K) germarium stained for α-spectrin and Vasa. While two GSCs are present in the control germarium, the mutant one contains only one GSC. GSCs are indicated by arrows. (L) Graph showing the relative percentage of germaria containing marked wild type control or <i>brm</i> or <i>bap180</i> mutant GSCs over a 3-week period ACI. Note that all initial percentages at day 2 ACI are normalized to 100%. (M) Graph showing that a gradual GSC loss is elicited by knocking down either <i>brm</i> or <i>bap180</i> in the germline.</p

Knock down of the PBAP complex subunits in the niche leads to a gradual GSC loss.

<p>(A–D) The control germaria (A, C) and mutant ones expressing <i>brm-Dominant-Negative</i> (<i>brm[K804R]</i>) (B) or <i>bap180-RNAi</i> transgene (D) under the control of <i>bab1-gal4</i>, stained for Vasa and α-spectrin. Only one GSC is present in the knockdown germarium at 14 days after eclosion (B, D), whereas the control germarium contains two GSCs (A, C). GSCs are indicated by arrows in all panels. (E, F) Graphs show that compared with the controls, knocking down <i>brm</i> (E) or the PBAP specific subunit encoding gene (<i>bap180</i> or <i>bap170</i>) (F) in the niche causes a significant drop of GSC number per germarium over a 2-week period after eclosion.</p

A Systematically Combined Genotype and Functional Combination Analysis of <i>CYP2E1</i>, <i>CYP2D6</i>, <i>CYP2C9</i>, <i>CYP2C19</i> in Different Geographic Areas of Mainland China – A Basis for Personalized Therapy

<div><p>The cytochrome P450 is the major enzyme involved in drug metabolism. Single <i>CYP</i> genotypes and metabolic phenotypes have been widely studied, but no combination analysis has been conducted in the context of specific populations and geographical areas. This study is the first to systematically analyze the combined genotypes and functional combinations of 400 samples of major <i>CYP</i> genes—<i>CYP2E1</i>, <i>CYP2D6</i>, <i>CYP2C9</i>, and <i>CYP2C19</i> in four geographical areas of mainland China. 167 different genotype combinations were identified, of which 25 had a greater than 1% frequency in the Chinese Han population. In addition, phenotypes of the four genes for each sample were in line with the predictions of previous studies of the four geographical areas. On the basis of the genotype classification, we were able to produce a systemic functional combinations analysis for the population. 25 of the combinations detected had at least two non-wild phenotypes and four showed a frequency above 1%. A bioinformatics analysis of the relationship between particular drugs and multi-genes was conducted. This is the first systematic study to analyze genotype combinations and functional combinations across whole Chinese population and could make a significant contribution in the field of personalized medicine and therapy.</p> </div