Structural Characterization and Expression Analysis of the SERK/SERL Gene Family in Rice (Oryza sativa)

Somatic embryogenesis (SE) is the developmental restructuring of somatic cells towards the embryogenic pathway and forms the basis of cellular totipotency in angiosperms. With the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encylopedia (KOME), we identified the leucine-rich repeat receptor-like kinase (LRR-RLK) genes from rice (Oryza sativa), which also encompasses genes involved in regulating somatic embryogenesis. Eight out of eleven of the rice SERK and SERL (SERK-like) genes have the TIGR annotation as (putative) brassinosteroid insensitive 1-associated receptor kinase (precursor). Real-time polymerase chain reaction analysis was undertaken to quantify transcript levels of these 11 genes. Most of these genes were upregulated by brassinosteroids although only a few of these displayed auxin induction. The expression profile of these genes is nearly uniform in the zygotic embryogenic tissue, but the expression pattern is more complex in the somatic embryogenic tissue. It is likely that OsSERKs and OsSERLs may be involved in somatic embryogenesis and also perform a role in morphogenesis and various other plant developmental processes. Functional validation of these somatic embryogenesis receptor-like kinase genes may help in elucidating their precise functions in regulating various facets of plant development

Characterization of three somatic embryogenesis receptor kinase genes from wheat, Triticum aestivum

We report here the isolation and characterization of three SOMATIC EMBRYOGENESIS RECEPTOR KINASE (TaSERK) genes from wheat. TaSERKs belong to a small family of receptor-like kinase genes, share a conserved structure and extensive sequence homology with previously reported plant SERK genes. TaSERK genes are in general auxin inducible and expressed during embryogenesis in cell cultures. We show here that somatic embryogenesis in Triticum aestivum is associated with high SERK expression which could be enhanced with auxin application and is calcium dependent. TaSERK transcripts could also be enhanced by epibrassinolide and abscisic acid. TaSERK1 and TaSERK2 may have a role in somatic embryogenesis, whereas TaSERK3 appears to be a brassinosteroid-associated kinase (BAK) lacking an SPP motif but shares a characteristic C-terminal domain with other SERK proteins. Also, the transcripts of all the three TaSERK genes could be induced in zygotic and somatic tissues. Although our analysis suggests them to be involved in somatic embryogenesis, they may have a broader role in acquiring embryogenic competence in wheat

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes

Impact of Job Complexity and Performance on CFO Compensation

Prior research suggests that Big 4 auditors provide higher quality audits by virtue of their large size. Still, the recent reforms mandated by the Sarbanes Oxley Act – by increasing client and auditor incentives for accurate reporting – may have narrowed audit quality differences across auditor groups. In this paper, we examine audit quality for Big 4 and Mid-tier auditors during 2003-06 and include clients of other smaller audit firms for comparison purposes. We examine actual audit quality (as proxied by earnings management metrics) as well as perceived audit quality (as proxied by the client- and year-specific eloading and ex ante equity risk premium metrics). We include in our analysis only those Big 4 clients for whom the Mid-tier firms are potentially viable as auditors. Relative to other smaller audit firm clients, we find Big 4 and Mid-tier audit clients to have (1) lower levels of accrual management, (2) higher levels of real earnings management, and (3) higher levels of investor-perceived accruals quality. In each case, we were unable to reject the null that Big 4 and Mid-tier audits are similar. However, we find Big 4 audit clients to have a lower client-specific ex ante equity risk premium relative to both Mid-tier and other smaller audit firm clients. Collectively, our findings indicate that in situations where a Mid-tier auditor is potentially viable, Big 4 clients could utilize a Mid-tier firm without adversely affecting audit quality. Still, the results suggest that Big 4 clients have a lower ex ante cost of equity capital which is likely related to the insurance considerations (“deep pockets”) – rather than the audit quality -- associated with having a Big 4 auditor.Auditor concentration, Audit quality, Earnings management, Cost of equity capital.

Cryptic blues: mechanism in sight!

Several plant responses are mediated by blue-light as also UV-A radiation. Until a few years ago, the identity of the blue/UV-A sensing photoreceptors was equivocal. In the past few years, however, the molecular genetic analysis of Arabidopsis mutants has greatly aided in the identification and characterization of blue/UV-A sensing cryptochrome 1 (cry1), cryptochrome 2 (cry2) and phototropin (JK224/ nph1). The cry1 and cry2 receptors, like DNA photolyases, are dual chromophore proteins and may harbour both a flavin (FAD) and a pterin for primarily regulating hypocotyl growth inhibition, cotyledon expansion and flowering time, besides sensing light for entraining endogenous clocks. In contrast, JK224/nph1 anchors another flavin, FMN, and regulates phototropism. In addition to flavins and pterin, evidence is mounting in favour of a carotenoid, zeaxanthin, for regulating blue-light-induced stomatal opening. There is little information on the signalling components acting downstream to blue sensory receptors, but nph1 has an intrinsic kinase domain that on photoexcitation initiates a phosphorelay through interaction with phosphoproteins like NPH3. Although the primary mechanism of action of cry1 and cry2 is unknown, their localization in the nucleus and protein-protein interaction with phytochromes indicates that they may directly regulate changes in gene expression. The occurrence of cryptochromes in both plants and animals indicates their ubiquitous nature and a prominent role in regulating diverse responses

Litigation Risk and Abnormal Accruals

In this paper, we examine the relation between auditor litigation risk and abnormal accruals over the 1989-2007 time period. We address potential endogeneity in prior studies by jointly modeling abnormal accruals and litigation risk in a simultaneous equation system. Our findings suggest that client-specific litigation risk affects auditor incentives to acquiesce to client demands for earnings management, i.e., the higher the risk of auditor litigation, the greater the auditor’s restraining influence on the abnormal accruals reported by the client. We also find evidence that abnormal accruals increase the likelihood of auditor litigation. We also document that the 1995 Public Securities Litigation Reform Act (PSLRA) lowered the client-specific risk of auditor litigation. Litigation reform remains a topic of ongoing interest. Our findings contribute to a better understanding of the effects of litigation reform (and related changes in legal exposure) on auditor incentives and earnings management.: Litigation risk, abnormal accruals, auditor incentives

Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis

Carotenoids, important lipid-soluble antioxidants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthesis genes, have been performed to get carotenoid-enriched rice grain. Study of genes involved in their biosynthesis can provide further information regarding the abundance/absence of carotenoids in different tissues. We have identified 16 and 34 carotenoid biosynthesis genes in rice and Populus genomes, respectively. A detailed analysis of the domain structure of carotenoid biosynthesis enzymes in rice, Populus and Arabidopsis has shown that highly conserved catalytic domains, along with other domains, are present in these proteins. Phylogenetic analysis of rice genes with Arabidopsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new functions. Expression of rice and Populus genes has been analyzed by full-length cDNA- and EST-based expression profiling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression profiling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have differential expression pattern during vegetative/reproductive development and are responsive to stress

An early auxin-responsive Aux/IAA gene from wheat (Triticum aestivum) is induced by epibrassinolide and differentially regulated by light and calcium

The plant hormone auxin plays a central role in regulating many aspects of plant growth and development. This largely occurs as a consequence of changes in gene expression. The Aux/IAA genes are best characterized among the early auxin-responsive genes, which encode short-lived transcriptional repressors. In most plants examined, including Arabidopsis, soybean, and rice, the Aux/IAA genes constitute a large gene family. By screening the available databases, at least 15 expressed sequence tags (ESTs) have been identified from wheat (Triticum aestivum), which exhibit high sequence identity with Aux/IAA homologues in other species. One of these Aux/IAA genes, TaIAA1, harbouring all the four conserved domains characteristic of the Aux/IAA proteins, has been characterized in detail. The expression of TaIAA1 is light-sensitive, tissue-specific, and is induced within 15-30 min of exogenous auxin application. Also, the TaIAA1 transcript levels increase in the presence of a divalent cation, Ca2+, and this effect is reversed by the calcium-chelating agent, EGTA. The TaIAA1 gene qualifies as the primary response gene because an increase in its transcript levels by auxin is unaffected by cycloheximide. In addition to auxin, the TaIAA1 gene is also induced by brassinosteroid, providing evidence that interplay between hormones is crucial for the regulation of plant growth and development

Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice

Auxin influences growth and development in plants by altering gene expression. Many auxin-responsive genes have been characterized in Arabidopsis in detail, but not in crop plants. Earlier, we reported the identification and characterization of the members of the GH3, Aux/IAA and SAUR gene families in rice. In this study, whole genome microarray analysis of auxin-responsive genes in rice was performed, with the aim of gaining some insight into the mechanism of auxin action. A comparison of expression profiles of untreated and auxin-treated rice seedlings identified 315 probe sets representing 298 (225 upregulated and 73 downregulated) unique genes as auxin-responsive. Functional categorization revealed that genes involved in various biological processes, including metabolism, transcription, signal transduction, and transport, are regulated by auxin. The expression profiles of auxin-responsive genes identified in this study and those of the members of the GH3, Aux/IAA, SAUR and ARF gene families were analyzed during various stages of vegetative and reproductive (panicle and seed) development by employing microarray analysis. Many of these genes are, indeed, expressed in a tissue-specific or developmental stage-specific manner, and the expression profiles of some of the representative genes were confirmed by real-time PCR. The differential expression of auxin-responsive genes during various stages of panicle and seed development implies their involvement in diverse developmental processes. Moreover, several auxin-responsive genes were differentially expressed under various abiotic stress conditions, indicating crosstalk between auxin and abiotic stress signaling