John C. Watson's research while affiliated with University of Maryland, College Park and other places

... The genes ycf3, clpP, rpoc1, and rpl2 have been found to have a variable number of introns among and within some taxonomic groups [23]. The gain or loss of introns in these genes have occurred independently in several linages of flowering plants [23,60]. However, no differences were found in the number of introns among the eight species; the ycf3, clpP, rpoc1, and rpl2 contain 2, 2, 1, and 0 introns, respectively. ...

... Nonetheless, the photoconversion cross-sections determined in vitro are not zero beyond 700 nm (Fig 1), indicating that some amount of P r will be converted into P fr during the night period with an application of NIR photons. The response of delayed flowering in two photosensitive species with the application of photons from an NIR LED is similar to classic very low fluence responses (VLFR), which require such low concentrations of P fr (phyA) that they are both irreversible and able to be induced by far-red [9,41]. Although some VLFRs can be induced by doses as low as 0.001 nmol m -2 [41], the intensity of full moonlight has been reported to range from 2 to 5 nmol m -2 s -1 [42,43]. ...

... Although introns are not protein coding, they play an important role in gene expression by regulating the rate of transcription, nuclear export, and stability of transcripts [46,47]. The loss of introns such as rpl2 and rps16 has been reported in the plant plastomes [48][49][50][51], but we did not find any evidence of this in the plastomes of Garcinia species. ...

... Fed-1, for example, is a small protein in PSI encoded by the nucleus. Upon illumination of white tissue, its transcript level increase phytochrome-dependent (Kaufman et al., 1985;Dobres et al., 1987), however in green tissue this gene is regulated on post-transcriptional level by altered transcript stability and translation (Elliott et al., 1989;Dickey et al., 1992;Petracek et al., 1998). A genome-wide study of polysome-bound mRNA on A. thaliana experiencing sudden dark revealed a general downregulation of polysomal loading. ...

... Thus, alternative gene assembly methods have been developed to address this bottleneck. An early technique used to synthesize ELPs was concatemerization (19), in which ELP monomer genes are ligated at overlapping sticky ends to create an oligomer within a vector. This method is simple and fast, but ligation with the parental plasmid can result in uncontrolled oligomerization (20,21). ...

... A leaf from each of the F 2 plants that had been phenotyped and a leaf from the parental lines were collected, lyophilised and ground with a TissueLyser (Quiagen). Genomic DNA was extracted with CTAB according to Watson and Thompson (1986), and working dilutions (20 ng ll -1 ) were prepared. SSR primer pair sequences were obtained from public sorghum databases (Bhattramakki et al. 2000; Kong et al. 2000; Schloss et al. 2002; Wang et al. 2012; Li et al. 2009; Brown et al. 1996; Upadhyaya et al. 2012) and synthesised in an external facility (Alfa DNA, Canada). ...

... For example, genomes uncoupled 4 (GUN4) is involved in the control of tetrapyrrole synthesis during the chlorophyll biosynthesis as a regulatory sub-unit of Mg-chelatase 9 , glutamyl-tRNA reductase family protein (HEMA1) is acutely dependent on phytochrome signaling and permitted the tetrapyrrole synthesis for the accumulation of chlorophyll 10 , and Mg-protoporphyrin IX methyltransferase (CHLM) plays a crucial role in chlorophyll biosynthesis and converts Mg-protoporphyrin IX to Mg-protoporphyrin IX monomethyl ester [11][12][13][14] . But recent research indicates that the chlorophyll a/b-binding (CAB) protein family is a crucial precursor signal during chlorophyll biosynthesis and metabolism 15,16 . At least 30 CAB family proteins have been found in Arabidopsis thaliana 17,18 , including photo-system protein 19 , one-helix protein 20 , and early light-induced proteins (ELIPs) 21 . ...

... This is evident in the work of Hafiz et al [52] who made it clear that DNA methylation plays a significant role in the transition from vegetative to reproductive growth and ploidy level of plants. Polymorphism in DNA methylation is an important form of genetic variation which plays a significant role in cell division, higher growth rate of plants, rooting ability and a potential capacity of silencing plant viruses [53][54]. ...

... In the green lineage, this approach has been used only for a few genes, including the maize Shrunken gene (Frommer and Starlinger, 1988), the maize histone H3 gene (Brignon et al., 1993), and the Arabidopsis Adh gene (Palas and Ferl, 1995). Information on plant chromatin structure was obtained mainly by DNaseI assays (e.g. Kaufman et al., 1987), which in combination with PCR also allowed to reveal chromatin structure at high resolution (Li et al., , 1999). Other, more recent approaches to determine chromatin structure in plants include restriction enzyme accessibility assays (Kalamajka et al., 2003) and chromatin immunoprecipitation (Chua et al., 2003; Zhang et al., 2003). ...

... As predicted by earlier biochemical studies (Reymond et al 1992), the maize and oat proteins were significantly smaller than the Arabidopsis protein, lacking several stretches of amino acids in the N-terminal domain. Partial nph1 sequences have also been reported for pea (Lin et al 1991, Lin & Watson 1992), ice plant (Mesembryanthemum crystallinum) (Bauer et al 1994), and spinach (GenBank Accession No. X73298). Christie et al (1998) resolved the photoreceptor question by demonstrating that nph1 expressed in insect cells grown in the dark exhibited blue-light-activated phosphorylation with the same fluence dependence and kinetics as the native Arabidopsis protein. ...