Dynamics of absorption properties of CDOM and its composition in Likas estuary, North Borneo, Malaysia

This is the final version. Available from Elsevier via the DOI in this record. Chromophoric Dissolved Organic Matter (CDOM) is a vital water constituent in aquatic ecosystems that contributes to water colour, affects light penetration, and impacts primary production. This study aims to determine the spatial and monsoonal variability of CDOM absorption properties in the Likas estuary, characterise the source of CDOM, and investigate the correlations between CDOM absorption properties and salinity. Likas estuary is a small estuary located in Kota Kinabalu city on the west coast of Sabah, facing the South China Sea. A mangrove ecosystem surrounds it with manufactured structures such as residential areas and public facilities. Surface water samples were collected at 19 stations: upstream of rivers to the river mouth and coastal area during spring tides every month, from June 2018 to July 2019, for 14-months. The distribution of aCDOM(440) in the study area is predictable as a signature in a coastal area with a decreasing gradient from the upstream towards coastal water (0.29 ± 0.19 m−1 to 1.05 ± 0.39 m−1). There are increasing spatial patterns of spectral slopes S275-295 and SR. However, S350-400 and S300-600 declined spatial gradients from the upstream to coastal water. Thus, S300-600 indicates a linear relationship between aCDOM(440), which unconventional results in coastal water. We suspect this is due to a small coverage of the study site with a distance of 0.5 m intervals of each station. This could be why the S300-600 had constant values throughout the study area (with no statistical difference between stations). In addition, S300-600 was merely varied in the stations located at the river mouth and coastal water. Based on the spectral slope ratio (SR), most of the stations located in the Darau, Inanam, and Bangka-Bangka rivers had SR values less than 1. Hence, CDOM in these stations is a terrestrial-dominated source. Therefore, from our observations during the study period, monsoonal variation could alter the source of CDOM in the study area.Universiti Malaysia SabahUniversiti Malaysia SabahMinistry of Higher Education of Malaysi

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

In Asian cultivated rice (Oryza sativa L.), aroma is one of the most valuable traits in grain quality and 2-ACP is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. Although the major locus for grain fragrance (frg gene) has been described recently in Basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different varieties is still limited. Here we report on characterisation of the frg gene in the Azucena variety, one of the few aromatic japonica cultivars. We used a RIL population from a cross between Azucena and IR64, a non-aromatic indica, the reference genomic sequence of Nipponbare (japonica) and 93–11 (indica) as well as an Azucena BAC library, to identify the major fragance gene in Azucena. We thus identified a betaine aldehyde dehydrogenase gene, badh2, as the candidate locus responsible for aroma, which presented exactly the same mutation as that identified in Basmati and Jasmine-like rices. Comparative genomic analyses showed very high sequence conservation between Azucena and Nipponbare BADH2, and a MITE was identified in the promotor region of the BADH2 allele in 93–11. The badh2 mutation and MITE were surveyed in a representative rice collection, including traditional aromatic and non-aromatic rice varieties, and strongly suggested a monophylogenetic origin of this badh2 mutation in Asian cultivated rices. Altogether these new data are discussed here in the light of current hypotheses on the origin of rice genetic diversity

Fluorescence-Tagged Transgenic Lines Reveal Genetic Defects in Pollen Growth—Application to the Eif3 Complex

BACKGROUND: Mutations in several subunits of eukaryotic translation initiation factor 3 (eIF3) cause male transmission defects in Arabidopsis thaliana. To identify the stage of pollen development at which eIF3 becomes essential it is desirable to examine viable pollen and distinguish mutant from wild type. To accomplish this we have developed a broadly applicable method to track mutant alleles that are not already tagged by a visible marker gene through the male lineage of Arabidopsis. METHODOLOGY/PRINCIPAL FINDINGS: Fluorescence tagged lines (FTLs) harbor a transgenic fluorescent protein gene (XFP) expressed by the pollen-specific LAT52 promoter at a defined chromosomal position. In the existing collection of FTLs there are enough XFP marker genes to track nearly every nuclear gene by virtue of its genetic linkage to a transgenic marker gene. Using FTLs in a quartet mutant, which yields mature pollen tetrads, we determined that the pollen transmission defect of the eif3h-1 allele is due to a combination of reduced pollen germination and reduced pollen tube elongation. We also detected reduced pollen germination for eif3e. However, neither eif3h nor eif3e, unlike other known gametophytic mutations, measurably disrupted the early stages of pollen maturation. CONCLUSION/SIGNIFICANCE: eIF3h and eIF3e both become essential during pollen germination, a stage of vigorous translation of newly transcribed mRNAs. These data delimit the end of the developmental window during which paternal rescue is still possible. Moreover, the FTL collection of mapped fluorescent protein transgenes represents an attractive resource for elucidating the pollen development phenotypes of any fine-mapped mutation in Arabidopsis

The Mw = 6.3, November 21, 2004, Les Saintes earthquake (Guadeloupe): Tectonic setting, slip model and static stress changes,

International audienceOn November 21, 2004, a magnitude 6.3 earthquake occurred offshore, 10 km south of Les Saintes archipelago in Guadeloupe (French West Indies). There were more than 30000 aftershocks recorded in the following two years, most of them at shallow depth near the islands of the archipelago. The main shock and its main aftershock of February 14, 2005 (Mw = 5.8) ruptured a NE-dipping normal fault (Roseau fault), mapped and identified as active from high-resolution bathymetric data a few years before. This fault belongs to an arc-parallel en echelon fault system that follows the inner edge of the northern part of the Lesser Antilles arc, accommodating the sinistral component of oblique convergence between the North American and Caribbean plates. The distribution of aftershocks and damage (destruction and landslides) are consistent with the main fault plane location and attitude. The slip model of the main shock, obtained by inverting jointly global broadband and local strong motion records, is characterized by two main slip zones located 5 to 10 km to the SE and NW of the hypocenter. The main shock is shown to have increased the Coulomb stress at the tips of the ruptured plane by more than 4 bars where most of the aftershocks occurred, implying that failures on fault system were mainly promoted by static stress changes. The earthquake also had an effect on volcanic activity since the Boiling Lake in Dominica drained twice, probably as a result of the extensional strain induced by the earthquake and its main aftershock

Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production

Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the dedifferentiation of microspores and conditioning the following androgenic response. In this study, we have used three barley doubled haploid lines with similar genetic background but different androgenic response. The Barley1 GeneChip was used for transcriptome comparison of these lines after mannitol stress treatment, allowing the identification of 213 differentially expressed genes. Most of these genes belong to the functional categories “cell rescue, defense, and virulence”; “metabolism”; “transcription”; and “transport”. These genes were grouped into clusters according to their expression profiles among lines. A principal component analysis allowed us to associate specific gene expression clusters to phenotypic variables. Genes associated with the ability of microspores to divide and form embryos were mainly involved in changes in the structure and function of membranes, efficient use of available energy sources, and cell fate. Genes related to stress response, transcription and translation regulation, and degradation of pollen-specific proteins were associated with green plant production, while expression of genes related to plastid development was associated with albino plant regeneration

Molecular Foundations of Reproductive Lethality in Arabidopsis thaliana

The SeedGenes database (www.seedgenes.org) contains information on more than 400 genes required for embryo development in Arabidopsis. Many of these EMBRYO-DEFECTIVE (EMB) genes encode proteins with an essential function required throughout the life cycle. This raises a fundamental question. Why does elimination of an essential gene in Arabidopsis often result in embryo lethality rather than gametophyte lethality? In other words, how do mutant (emb) gametophytes survive and participate in fertilization when an essential cellular function is disrupted? Furthermore, why do some mutant embryos proceed further in development than others? To address these questions, we first established a curated dataset of genes required for gametophyte development in Arabidopsis based on information extracted from the literature. This provided a basis for comparison with EMB genes obtained from the SeedGenes dataset. We also identified genes that exhibited both embryo and gametophyte defects when disrupted by a loss-of-function mutation. We then evaluated the relationship between mutant phenotype, gene redundancy, mutant allele strength, gene expression pattern, protein function, and intracellular protein localization to determine what factors influence the phenotypes of lethal mutants in Arabidopsis. After removing cases where continued development potentially resulted from gene redundancy or residual function of a weak mutant allele, we identified numerous examples of viable mutant (emb) gametophytes that required further explanation. We propose that the presence of gene products derived from transcription in diploid (heterozygous) sporocytes often enables mutant gametophytes to survive the loss of an essential gene in Arabidopsis. Whether gene disruption results in embryo or gametophyte lethality therefore depends in part on the ability of residual, parental gene products to support gametophyte development. We also highlight here 70 preglobular embryo mutants with a zygotic pattern of inheritance, which provide valuable insights into the maternal-to-zygotic transition in Arabidopsis and the timing of paternal gene activation during embryo development

Behavioural observations in gunn rats

The Gunn rat is a hooded mutant of albino rat with various biochemical defects, including a low UDP-glucuronosyl-transferase activity. As a consequence, about half of their offspring are jaundiced from birth, due to high free bilirubin levels, and develop widespread brain damage. The behaviour of both jaundiced and nonjaundiced Gunn rats was studied in four different tests in a shuttle-box and in a stepthrough passive avoidance situation, and compared with that of normal hooded rats. No differences among groups were found in performance of shuttle responses to a tone in a pseudoconditioning paradigm in which tones and shocks were given at random. However, rats from the two Gunn groups made less shuttlings to the tone in two tests that involved an avoidance contingency (each response cancelled one shock). In addition, nonicteric Gunn rats also performed poorly in a classical conditioning test in the shuttle-box (tones and shocks paired on every trial regardless of responses). This last deficiency of non-icteric Gunn rats may be explained by their higher tendency to freeze in situations involving stimulus-stimulus interactions. They also showed a higher latency than that of the two other groups to enter the dark side of the step-through apparatus on their first exposure to it. All animals seemed to learn the passive-avoidance task to the same extent, however, as shown in a retest carried out 48 h later. Both Gunn groups were hypersensitive to the stereotyped-behaviour-inducing action of apomorphine (0.125–1.0 mg/kg, i.p.), but all groups were about equally sensitive to that of d -amphetamine sulfate (0.5–4.0 mg/kg). Since apomorphine is disposed of by glucuronidation, this might be explained by the low UDP-glucuronosyl-transferase activity known to exist in the Gunn animals. The present results show that additional genetic defects have developed by in-breeding in the Gunn population, which are unrelated to brain damage caused by bilirubin, and which can be well characterized from a behavioural standpoint.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46403/1/213_2004_Article_BF00426881.pd

Organization and molecular evolution of a disease-resistance gene cluster in coffee trees

<p>Abstract</p> <p>Background</p> <p>Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (<it>Coffea arabica</it>), a region spanning the <it>S</it>_<it>H</it><it>3 </it>locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the <it>S</it>_<it>H</it><it>3 </it>locus.</p> <p>Results</p> <p>Sequence analysis of the <it>S</it>_<it>H</it><it>3 </it>region in three coffee genomes, E^aand C^asubgenomes from the allotetraploid <it>C. arabica </it>and C^cgenome from the diploid <it>C. canephora</it>, revealed the presence of 5, 3 and 4 R genes in E^a, C^a, and C^cgenomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the <it>S</it>_<it>H</it><it>3 </it>locus in <it>C. arabica</it>. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the <it>S</it>_<it>H</it><it>3</it>-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the <it>S</it>_<it>H</it><it>3 </it>locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of <it>C. arabica</it>. Significant positive selection was detected in the solvent-exposed residues of the <it>S</it>_<it>H</it><it>3</it>-CNL copies.</p> <p>Conclusion</p> <p>The ancestral <it>S</it>_<it>H</it><it>3</it>-CNL copy was inserted in the <it>S</it>_<it>H</it><it>3 </it>locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the <it>S</it>_<it>H</it><it>3</it>-CNL copies predates the divergence between <it>Coffea </it>species. The <it>S</it>_<it>H</it><it>3</it>-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the <it>S</it>_<it>H</it><it>3 </it>locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of <it>S</it>_<it>H</it><it>3</it>-CNL in coffee trees.</p