ALBERT

Description: OsWUS has recently been shown to be a transcription factor gene critical for tiller development and fertility in rice. The OsWUS protein consists of three conserved structural domains, but their biological functions are still unclear. We discovered a new rice mutant resulting from tissue culture, which hardly produced tillers and exhibited complete female sterility. The male and female floral organs of the mutant were morphologically indistinguishable from those of the wild type. We named the mutant srt1 for completely s terile and r educed t illering 1. Map-based cloning revealed that the mutant phenotypes were caused by a mutation in OsWUS . Compared with the two previously reported null allelic mutants of OsWUS ( tab1-1 and moc3-1 ), which could produce partial N-terminal peptides of OsWUS, the srt1 protein contained a deletion of only seven amino acids within the conserved homeobox domain of OsWUS. However, the mutant phenotypes (monoculm and female sterility) displayed in srt1 were as typical and severe as those in tab1-1 and moc3-1 . This indicates that the homeobox domain of SRT1 is essential for the regulation of tillering and sterility in rice. In addition, srt1 showed an opposite effect on panicle development to that of the two null allelic mutants, implying that the srt1 protein might still have partial or even new functions on panicle development. The results of this study suggest that the homeobox domain is pivotal for OsWUS function.

Description: High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum . The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal x Seemann, G. mustelinum Miers x Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F 2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

Description: The E2F transcription factors are important regulators of the cell cycle whose function is commonly misregulated in cancer. To identify novel regulators of E2F1 activity in vivo , we used Drosophila to conduct genetic screens. For this, we generated transgenic lines that allow the tissue-specific depletion of dE2F1 by RNAi. Expression of these transgenes using Gal4 drivers in the eyes and wings generated reliable and modifiable phenotypes. We then conducted genetic screens testing the capacity of Exelixis deficiencies to modify these E2F1-RNAi phenotypes. From these screens, we identified mutant alleles of Suppressor of zeste 2 [ Su(z)2 ] and multiple Polycomb group genes as strong suppressors of the E2F1-RNA interference phenotypes. In validation of our genetic data, we find that depleting Su(z)2 in cultured Drosophila cells restores the cell-proliferation defects caused by reduction of dE2F1 by elevating the level of dE2f1 . Furthermore, analyses of methylation status of histone H3 lysine 27 (H3K27me) from the published modENCODE data sets suggest that the genomic regions harboring dE2f1 gene and certain dE2f1 target genes display H3K27me during development and in several Drosophila cell lines. These in vivo observations suggest that the Polycomb group may regulate cell proliferation by repressing the transcription of dE2f1 and certain dE2F1 target genes. This mechanism may play an important role in coordinating cellular differentiation and proliferation during Drosophila development.

Description: Physical appearance traits, such as feather-crested head, comb size and type, beard, wattles size, and feathered feet, are used to distinguish between breeds of chicken and also may be associated with economic traits. In this study, a genome-wide linkage analysis was used to identify candidate regions and genes for physical appearance traits and to potentially provide further knowledge of the molecular mechanisms that underlie these traits. The linkage analysis was conducted with an F2 population derived from Beijing-You chickens and a commercial broiler line. Single-nucleotide polymorphisms were analyzed using the Illumina 60K Chicken SNP Beadchip. The data were used to map quantitative trait loci and genes for six physical appearance traits. A 10-cM/0.51-Mb region (0.0–10.0 cM/0.00–0.51 Mb) with 1% genome-wide significant level on LGE22C19W28_E50C23 linkage group (LGE22) for crest trait was identified, which is likely very closely linked to the HOXC8 . A QTL with 5% chromosome-wide significant level for comb weight, which partly overlaps with a region identified in a previous study, was identified at 74 cM/25.55 Mb on chicken ( Gallus gallus ; GG) chromosome 3 ( i.e. , GGA3). For beard and wattles traits, an identical region 11 cM/2.23 Mb (0.0–11.0 cM/0.00–2.23 Mb) including WNT3 and GH genes on GGA27 was identified. Two QTL with 1% genome-wide significant level for feathered feet trait, one 9-cM/2.80-Mb (48.0-57.0/13.40-16.20 Mb) region on GGA13, and another 12-cM/1.45-Mb (41.0–53.0 cM/11.37–12.82 Mb) region on GGA15 were identified. These candidate regions and genes provide important genetic information for the physical appearance traits in chicken.

Description: Polydactyly occurs in some chicken breeds, but the molecular mechanism remains incompletely understood. Combined genome-wide linkage analysis and association study (GWAS) for chicken polydactyly helps identify loci or candidate genes for the trait and potentially provides further mechanistic understanding of this phenotype in chickens and perhaps other species. The linkage analysis and GWAS for polydactyly was conducted using an F2 population derived from Beijing-You chickens and commercial broilers. The results identified two QTLs through linkage analysis and seven single-nucleotide polymorphisms (SNPs) through GWAS, associated with the polydactyly trait. One QTL located at 35 cM on the GGA2 was significant at the 1% genome-wise level and another QTL at the 1% chromosome-wide significance level was detected at 39 cM on GGA19. A total of seven SNPs, four of 5% genome-wide significance (P 〈 2.98 x 10 –6 ) and three of suggestive significance (5.96 x 10 –5 ) were identified, including two SNPs (GGaluGA132178 and Gga_rs14135036) in the QTL on GGA2. Of the identified SNPs, the eight nearest genes were sonic hedgehog ( SHH ), limb region 1 homolog (mouse) ( LMBR1 ), dipeptidyl-peptidase 6, transcript variant 3 ( DPP6 ), thyroid-stimulating hormone, beta ( TSHB ), sal-like 4 (Drosophila) ( SALL4 ), par-6 partitioning defective 6 homolog beta ( Caenorhabditis elegans ) ( PARD6B ), coenzyme Q5 ( COQ5 ), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, etapolypeptide ( YWHAH ). The GWAS supports earlier reports of the importance of SHH and LMBR1 as regulating genes for polydactyly in chickens and other species, and identified others, most of which have not previously been associated with limb development. The genes and associated SNPs revealed here provide detailed information for further exploring the molecular and developmental mechanisms underlying polydactyly.

Description: The sampling artifacts (both positive and negative) and the influence of thermal-optical methods (both charring correction method and the peak inert mode temperature) on the split of organic carbon (OC) and elemental carbon (EC) were evaluated in Beijing. The positive sampling artifact constituted 10% and 23% of OC concentration determined by the bare quartz filter during winter and summer, respectively. For summer samples, the adsorbed gaseous organics were found to continuously evolve off the filter during the whole inert mode when analyzed by the IMPROVE-A temperature protocol. This may be due to the oxidation of the adsorbed organics during sampling (reaction artifact) which would increase their thermal stability. The backup quartz approach was evaluated by a denuder-based method for assessing the positive artifact. The quartz-quartz (QBQ) in series method was demonstrated to be reliable, since all of the OC collected by QBQ was from originally gaseous organics. Negative artifact that could be adsorbed by quartz filter was negligible. When the activated carbon impregnated glass fiber (CIG) filter was used as the denuded backup filter, the denuder efficiency for removing gaseous organics that could be adsorbed by the CIG filter was only about 30%. EC values were found to differ by a factor of about two depending on the charring correction method. Influence of the peak inert mode temperature was evaluated based on the summer samples. The EC value was found to continuously decrease with the peak inert mode temperature. Premature evolution of light absorbing carbon began when the peak inert mode temperature was increased from 580 to 650 °C; when further increased to 800 °C, the OC and EC split frequently occurred in the He mode, and the last OC peak was characterized by the overlapping of two separate peaks. The discrepancy between EC values defined by different temperature protocols was larger for Beijing carbonaceous aerosol compared with North America and Europe, perhaps due to the higher concentration of brown carbon in Beijing aerosol.

Description: Aged smoke from a prescribed fire (dominated by conifers) impacted Atlanta, GA on 28 February 2007 and dramatically increased hourly ambient concentrations of PM2.5 and organic carbon (OC) up to 140 and 72 μg m−3, respectively. It was estimated that over 1 million residents were exposed to the smoky air lasting from the late afternoon to midnight. To better understand the processes impacting the aging of fire plumes, a detailed chemical speciation of carbonaceous aerosols was conducted by gas chromatography/mass spectrometry (GC/MS) analysis. Ambient concentrations of many organic species (levoglucosan, resin acids, retene, n-alkanes and n-alkanoic acids) associated with wood burning emission were significantly elevated on the event day. Levoglucosan increased by a factor of 10, while hopanes, steranes, cholesterol and major polycyclic aromatic hydrocarbons (PAHs) did not show obvious increases. Strong odd over even carbon number predominance was found for n-alkanes versus even over odd predominance for n-alkanoic acids. Alteration of resin acids during transport from burning sites to monitors is suggested by the observations. Our study also suggests that large quantities of biogenic volatile organic compounds (VOCs) and semivolatile organic compounds (SVOCs) were released both as products of combustion and unburned vegetation heated by the fire. Higher leaf temperature can stimulate biogenic VOC and SVOC emissions, which enhanced formation of secondary organic aerosols (SOA) in the atmosphere. This is supported by elevated ambient concentrations of secondary organic tracers (dicarboxylic acids, 2-methyltetrols, pinonic acid and pinic acid). An approximate source profile was built for the aged fire plume to help better understand evolution of wood smoke emission and for use in source impact assessment.

Description: The sampling artifacts (both positive and negative) and the influence of thermal-optical methods (both charring correction method and the peak inert mode temperature) on the split of organic carbon (OC) and elemental carbon (EC) were evaluated in Beijing. The positive sampling artifact constituted 10% and 23% of OC concentration determined by the bare quartz filter during winter and summer, respectively. For summer samples, the adsorbed gaseous organics were found to continuously evolve off the filter during the whole inert mode when analyzed by the IMPROVE-A temperature protocol. This may be due to the oxidation of the adsorbed organics during sampling (reaction artifact) which would increase their thermal stability. The backup quartz approach was evaluated by a denuder-based method for assessing the positive artifact. The quartz-quartz (QBQ) in series method was demonstrated to be reliable, since all of the OC collected by QBQ was from originally gaseous organics. Negative artifact that could be adsorbed by quartz filter was negligible. When the activated carbon impregnated glass fiber (CIG) filter was used as the denuded backup filter, the denuder efficiency for removing gaseous organics that could be adsorbed by the CIG filter was only about 30%. EC values were found to differ by a factor of about two depending on the charring correction method. Influence of the peak inert mode temperature was evaluated based on the summer samples. The EC value was found to continuously decrease with the peak inert mode temperature. Premature evolution of light absorbing carbon began when the peak inert mode temperature was increased from 580 to 650 °C; when further increased to 800 °C, the OC and EC split frequently occurred in the He mode, and the last OC peak was characterized by the overlapping of two separate peaks. The discrepancy between EC values defined by different temperature protocols was larger for Beijing carbonaceous aerosol compared with North America and Europe, perhaps due to the higher concentration of brown carbon in Beijing aerosol.

Description: Size-resolved chemical compositions of non-refractory submicron aerosol were measured using an Aerodyne quadrupole aerosol mass spectrometer (Q-AMS) at the rural site Back Garden (BG), located ~50 km northwest of Guangzhou in July 2006. This paper characterized the submicron aerosol particles of regional air pollution in Pearl River Delta (PRD) in the southern China. Organics and sulfate dominated the submicron aerosol compositions, with average mass concentrations of 11.8 ± 8.4 μg m−3 and 13.5 ± 8.7 μg m−3, respectively. Unlike other air masses, the air masses originated from Southeast-South and passing through the PRD urban areas exhibited distinct bimodal size distribution characteristics for both organics and sulfate: the first mode peaked at vacuum aerodynamic diameters (Dva) ∼200 nm and the second mode occurred at Dva from 300–700 nm. With the information from AMS, it was found from this study that the first mode of organics in PRD regional air masses was contributed by both secondary organic aerosol formation and combustion-related emissions, which is different from most findings in other urban areas (first mode of organics primarily from combustion-related emissions). The analysis of AMS mass spectra data by positive matrix factorization (PMF) model identified three sources of submicron organic aerosol including hydrocarbon-like organic aerosol (HOA), low volatility oxygenated organic aerosol (LV-OOA) and semi-volatile oxygenated organic aerosol (SV-OOA). The strong correlation between HOA and EC indicated primary combustion emissions as the major source of HOA while a close correlation between SV-OOA and semi-volatile secondary species nitrate as well as between LV-OOA and nonvolatile secondary species sulfate suggested secondary aerosol formation as the major source of SV-OOA and LV-OOA at the BG site. However, LV-OOA was more aged than SV-OOA as its spectra was highly correlated with the reference spectra of fulvic acid, an indicator of aged and oxygenated aerosol. The origin of HOA and OOA (the sum of LV-OOA and SV-OOA) has been further confirmed by the statistics that primary organic carbon (POC) and secondary organic carbon (SOC), estimated by the EC tracer method, were closely correlated with HOA and OOA, respectively. The results of the EC tracer method and of the PMF model revealed that primary organic aerosol (POA) constituted ~34–47 % of OA mass and secondary organic aerosol (SOA) constituted ~53–66 % of regional organic aerosol in PRD during summer season. The presence of abundant SOA was consistent with water soluble organic carbon (WSOC) results (accounting for ~60 % of OC on average) by Miyazaki et al. (2009) for the same campaign. OOA correlated well with WSOC at the BG site, indicating that most OOA were water soluble. More specifically, approximately 86 % of LV-OOA and 61 % of SV-OOA were estimated as water soluble species on the basis of carbon content comparison.

Description: An improved Gas and Aerosol Collector (GAC) equipped with a newly designed aerosol collector and a set of dull-polished wet annular denuder (WAD) was developed based on a Steam Jet Aerosol Collector (SJAC) sampler. Combined with Ion Chromatography (IC) the new sampler performed well in laboratory tests with high collection efficiencies for SO2 (above 98%) and particulate sulfate (as high as 99.5%). An inter-comparison between the GAC-IC system and the filter-pack method was performed and the results indicated that the GAC-IC system could supply reliable particulate sulfate, nitrate, chloride, and ammonium data in field measurement with a much wider range of ambient concentrations. When applied in two major field campaigns (rural and coastal sites) in China, the GAC-IC system provided high-quality data in ambient conditions even under high loadings of pollutants. Its measurements were highly correlated with data by other commercial instruments such as the SO2 analyzer (43c, Thermo-Fisher, USA; R2 as 0.96), the HONO analyzer (LOPAP, Germany; R2 as 0.91 for samples from 15:00 to 07:00), a filter sampler (Tianhong, China; R2 as 0.86 for SO42−), and Aerosol Mass Spectrometer (AMS, Aerodyne, USA; R2 above 0.77 for major species) over a wide range of concentrations. Through the application of the GAC-IC system, it was identified that 70% of chloride and nitrate by the filter method could be lost during daytime sampling due to high temperature in the rural site of Kaiping. In Changdao field campaign (coastal site), though a particle dryer was applied, its drying efficiency was not well considered for the collection efficiency of AMS seemed still interfered a bit by local high relative humidity. If the inter-comparison was done with relative humidity below 50%, the correlations ranged from 0.81 to 0.94 for major species. Through laboratory and field studies, this instrument is proved particularly useful in future intensive campaigns or long-term monitoring stations to study various environmental issues such as secondary aerosol and haze formation, as well as climate change.