The independence of neutral and ionized gas outflows in low-z galaxies

Using a large sample of emission line galaxies selected from the Sloan Digital Sky Survey, we investigate the kinematics of the neutral gas in the interstellar medium (ISM) based on the Na I$\lambda\lambda$5890,5896 (Na D) doublet absorption line. By removing the Na D contribution from stellar atmospheres, we isolate the line profile of the Na D excess, which represents the neutral gas in the ISM. The kinematics traced by the Na D excess show high velocity and velocity dispersion for a fraction of galaxies, indicating the presence of neutral gas outflows. We find that the kinematics measured from the Na D excess are similar between AGNs and star-forming galaxies. Moreover, by comparing the kinematics traced by the Na D excess and those by the [O III]$\lambda$5007 line taken from Woo et al. (2017), which traces ionized outflows driven by AGNs, we find no correlation between them. These results demonstrate that the neutral gas in the ISM traced by the Na D excess and the ionized gas traced by [O III] are kinematically independent, and AGN has no impact on the neutral gas outflows. In contrast to [O III], we find that the measured line-of-sight velocity shift and velocity dispersion of the Na D excess increase for more face-on galaxies due to the projection effect, supporting that Na D outflows are radially driven (i.e., perpendicular to the major axis of galaxies), presumably due to star formation.Comment: 7 pages, 6 figures; Accepted for publication in ApJ, corrected the titl

Charge redistribution and local lattice structure of (F, Zn)-codoped LaFeAsO superconductor

To understand the abnormal behavior of the superconducting transition temperature (T-c) because of the presence of a non-magnetic Zn impurity in the (F, Zn)-codoped LaFeAsO system (Li et al 2010 New J. Phys. 12 083008), we investigated its unique electronic and local structures via x-ray absorption spectroscopy and first-principles calculations. The data obtained showed that the presence of a Zn impurity induces an electron transfer from As to Fe atoms in both the F-underdoped and -overdoped regions. Moreover, due to the lattice mismatch, the local lattice structure is finely modulated by both F and Zn impurities. Actually, in the F-underdoped region doping by Zn is associated with regular FeAs4 tetrahedra, while distorted FeAs4 tetrahedra occur in the F-overdoped region where superconductivity is significantly suppressed

A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

Plasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of ArinaLrFor, an Lr14a-containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca2+-permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a. Haplotype analyses indicate that Lr14a-containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding

A Dominant X-Linked QTL Regulating Pubertal Timing in Mice Found by Whole Genome Scanning and Modified Interval-Specific Congenic Strain Analysis

BACKGROUND: Pubertal timing in mammals is triggered by reactivation of the hypothalamic-pituitary-gonadal (HPG) axis and modulated by both genetic and environmental factors. Strain-dependent differences in vaginal opening among inbred mouse strains suggest that genetic background contribute significantly to the puberty timing, although the exact mechanism remains unknown. METHODOLOGY/PRINCIPAL FINDINGS: We performed a genome-wide scanning for linkage in reciprocal crosses between two strains, C3H/HeJ (C3H) and C57BL6/J (B6), which differed significantly in the pubertal timing. Vaginal opening (VO) was used to characterize pubertal timing in female mice, and the age at VO of all female mice (two parental strains, F1 and F2 progeny) was recorded. A genome-wide search was performed in 260 phenotypically extreme F2 mice out of 464 female progeny of the F1 intercrosses to identify quantitative trait loci (QTLs) controlling this trait. A QTL significantly associated was mapped to the DXMit166 marker (15.5 cM, LOD = 3.86, p<0.01) in the reciprocal cross population (C3HB6F2). This QTL contributed 2.1 days to the timing of VO, which accounted for 32.31% of the difference between the original strains. Further study showed that the QTL was B6-dominant and explained 10.5% of variation to this trait with a power of 99.4% at an alpha level of 0.05.The location of the significant ChrX QTL found by genome scanning was then fine-mapped to a region of approximately 2.5 cM between marker DXMit68 and rs29053133 by generating and phenotyping a panel of 10 modified interval-specific congenic strains (mISCSs). CONCLUSIONS/SIGNIFICANCE: Such findings in our study lay a foundation for positional cloning of genes regulating the timing of puberty, and also reveal the fact that chromosome X (the sex chromosome) does carry gene(s) which take part in the regulative pathway of the pubertal timing in mice

Genetic characterization of natural variation regulating thermal responses in plant development

Temperature affects several aspects of plant growth and development. The predicted rises in global temperature is expected to have an impact on worldwide crop productivity. Plants alter their physiological and developmental strategies in order to survive day to day and seasonal fluctuation in their growth temperature. In order to predict the impact of temperature on plants and to develop varieties that can cope with varied temperatures, we need to have a better knowledge of temperature response in plants at the molecular level. It is currently unclear as to how plants perceive and respond to varying temperatures. In this thesis, I employed model plant Arabidopsis thaliana as a tool to identify new factors involved in this process in plants. In this thesis, I have screened for natural variation in Arabidopsis accessions in temperature-response, followed by gene identification and characterization. First, Cvi-0, collected from Cape Verde Island, was identified to be insensitive to higher temperature. Using Quantitative Trait Loci (QTL) mapping with recombinant inbred lines derived from a cross between Cvi-0 and the reference strain Col-0 (CviColRILs), I showed that a QTL tightly linked to the blue light receptor CRYTOCHROMOME 2 (CRY2) contributes to natural variation in hypocotyl elongation and flowering response to temperature. The role for the CviCRY2 allele in response to temperature was supported by quantitative knockdown experiment with artificial microRNAs (amiRNAs) in Cvi-0. In addition, transgenic complementation experiments with CviCRY2 allele in the Ler-0, Col-0 and cry2 mutant backgrounds suggest that the role of CRY2 in regulating temperature response is dependent on the genetic background indicating the presence of modifiers for this response. Second, I discovered that Sij4 strain, collected from central Asia, is insensitive to temperature-induced hypocotyl elongation, and displays a temperature-dependent growth defect in their first leaves (thus named “abnormal first leaves (afl)”). Both traits show high genetic correlation (afl) (rG=0.88) indicating common genetic basis. Using Sij4ColF2 and Sij4LerF2 populations, I fine mapped the AFL locus to a 6 kb fragment, which includes a previously uncharacterized gene At2g31580. I demonstrate At2g31580 is AFL through transgenic complementation and artificial microRNA mediated knock-down experiments. I show that AFL regulates cell cycle at the G2/M transition through a combination of flow cytometry, transcriptome analysis and by using the cell cycle marker CYCB1. CyclinB1,1 (CYCB1,1), a key gene in the regulation of cell cycle, was not mis-expressed on transcriptional level, but a strong pCYCB1,1-CYCB1,1-GFP signal accumulated in mutant cells suggested that inhibition of CYCB1,1 degrading during G2/M phase transition. This was associated with increased DNA content suggestive of endoreduplication. Furthermore, I have shown that plants compromised for AFL function are more prone to DNA damage, suggesting a role for AFL in DNA repair. In summary, my studies on natural genetic variation in Arabidopsis identify a new factor AFL in regulating cell elongation and cell proliferation in response to higher temperature. In this thesis I review temperature response in plants and then report novel functions for two genes, CRY2 and AFL, in higher temperature response. In the first chapter I review our understanding of temperature response in plants and the associated mechanisms. I also provide an introduction to natural variation in Arabidopsis. In the second chapter I describe the results from screen I have carried out to find natural variants with altered thermal response and then go on describe the genetic basis of the temperature insensitivity phenotype in the Cvi-0 strain of Arabidopsis thaliana. In Chapter 3, I describe the genetic and molecular basis of temperature insensitivity in Sij-4, another strain I picked up from the screen. The natural afl mutant allele in Sij4 can be used as system to address fundamental questions of AFL beyond temperature response such as cell cycle regulation in plants. My finding on CRY2 opens up avenues for studying temperature and light interactions. The implications of this study as well as future areas for research are also discusses

Genetic characterization of natural variation regulating thermal responses in plant development

Temperature affects several aspects of plant growth and development. The predicted rises in global temperature is expected to have an impact on worldwide crop productivity. Plants alter their physiological and developmental strategies in order to survive day to day and seasonal fluctuation in their growth temperature. In order to predict the impact of temperature on plants and to develop varieties that can cope with varied temperatures, we need to have a better knowledge of temperature response in plants at the molecular level. It is currently unclear as to how plants perceive and respond to varying temperatures. In this thesis, I employed model plant Arabidopsis thaliana as a tool to identify new factors involved in this process in plants. In this thesis, I have screened for natural variation in Arabidopsis accessions in temperature-response, followed by gene identification and characterization. First, Cvi-0, collected from Cape Verde Island, was identified to be insensitive to higher temperature. Using Quantitative Trait Loci (QTL) mapping with recombinant inbred lines derived from a cross between Cvi-0 and the reference strain Col-0 (CviColRILs), I showed that a QTL tightly linked to the blue light receptor CRYTOCHROMOME 2 (CRY2) contributes to natural variation in hypocotyl elongation and flowering response to temperature. The role for the CviCRY2 allele in response to temperature was supported by quantitative knockdown experiment with artificial microRNAs (amiRNAs) in Cvi-0. In addition, transgenic complementation experiments with CviCRY2 allele in the Ler-0, Col-0 and cry2 mutant backgrounds suggest that the role of CRY2 in regulating temperature response is dependent on the genetic background indicating the presence of modifiers for this response. Second, I discovered that Sij4 strain, collected from central Asia, is insensitive to temperature-induced hypocotyl elongation, and displays a temperature-dependent growth defect in their first leaves (thus named “abnormal first leaves (afl)”). Both traits show high genetic correlation (afl) (rG=0.88) indicating common genetic basis. Using Sij4ColF2 and Sij4LerF2 populations, I fine mapped the AFL locus to a 6 kb fragment, which includes a previously uncharacterized gene At2g31580. I demonstrate At2g31580 is AFL through transgenic complementation and artificial microRNA mediated knock-down experiments. I show that AFL regulates cell cycle at the G2/M transition through a combination of flow cytometry, transcriptome analysis and by using the cell cycle marker CYCB1. CyclinB1,1 (CYCB1,1), a key gene in the regulation of cell cycle, was not mis-expressed on transcriptional level, but a strong pCYCB1,1-CYCB1,1-GFP signal accumulated in mutant cells suggested that inhibition of CYCB1,1 degrading during G2/M phase transition. This was associated with increased DNA content suggestive of endoreduplication. Furthermore, I have shown that plants compromised for AFL function are more prone to DNA damage, suggesting a role for AFL in DNA repair. In summary, my studies on natural genetic variation in Arabidopsis identify a new factor AFL in regulating cell elongation and cell proliferation in response to higher temperature. In this thesis I review temperature response in plants and then report novel functions for two genes, CRY2 and AFL, in higher temperature response. In the first chapter I review our understanding of temperature response in plants and the associated mechanisms. I also provide an introduction to natural variation in Arabidopsis. In the second chapter I describe the results from screen I have carried out to find natural variants with altered thermal response and then go on describe the genetic basis of the temperature insensitivity phenotype in the Cvi-0 strain of Arabidopsis thaliana. In Chapter 3, I describe the genetic and molecular basis of temperature insensitivity in Sij-4, another strain I picked up from the screen. The natural afl mutant allele in Sij4 can be used as system to address fundamental questions of AFL beyond temperature response such as cell cycle regulation in plants. My finding on CRY2 opens up avenues for studying temperature and light interactions. The implications of this study as well as future areas for research are also discusses