Where the Guesswork Ends and the Accrual Begins: Environmental Remediation Liabilities and Their Effects on the Managerial Decision-Making Process

Environmental remediation is not new, but accounting for the costs of such a process is. In 1996, the first authoritative literature on accounting for the costs of cleaning up environmental degradation were established, and they gave insight into the accounting treatment for environmental remediation liabilities (ERLs). The aim of the thesis is to explain the new accrual methods for ERLs and show their importance as they have influenced many managerial philosophies. The thesis also examines some of the weaknesses of ERLs and illustrates possible changes for the future. The most important aspect of ERLs is that they have helped management begin to account for the costs of environmental degradation. In turn, companies are starting to change many of the policies they have concerning these clean-up costs. What this begins to illustrate, then, is that accounting policies may have a direct effect on how companies do business, and, therefore, the accounting profession needs to take a closer look at how it values the environment

Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate.

Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than in differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-β and BMP signaling, which we found NMD acts through to influence definitive endoderm versus mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages

A Upf3b-mutant mouse model with behavioral and neurogenesis defects.

Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA degradation pathway that acts on RNAs terminating their reading frames in specific contexts. NMD is regulated in a tissue-specific and developmentally controlled manner, raising the possibility that it influences developmental events. Indeed, loss or depletion of NMD factors have been shown to disrupt developmental events in organisms spanning the phylogenetic scale. In humans, mutations in the NMD factor gene, UPF3B, cause intellectual disability (ID) and are strongly associated with autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD) and schizophrenia (SCZ). Here, we report the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition (PPI), a measure of sensorimotor gating commonly deficient in individuals with SCZ and other brain disorders. Consistent with both their PPI and learning defects, cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo. In addition, neural stem cells from Upf3b-null mice have impaired ability to undergo differentiation and require prolonged culture to give rise to functional neurons with electrical activity. RNA sequencing (RNAseq) analysis of the frontal cortex identified UPF3B-regulated RNAs, including direct NMD target transcripts encoding proteins with known functions in neural differentiation, maturation and disease. We suggest Upf3b-null mice serve as a novel model system to decipher cellular and molecular defects underlying ID and neurodevelopmental disorders

A microRNA cluster in the Fragile-X region expressed during spermatogenesis targets FMR1.

Testis-expressed X-linked genes typically evolve rapidly. Here, we report on a testis-expressed X-linked microRNA (miRNA) cluster that despite rapid alterations in sequence has retained its position in the Fragile-X region of the X chromosome in placental mammals. Surprisingly, the miRNAs encoded by this cluster (Fx-mir) have a predilection for targeting the immediately adjacent gene, Fmr1, an unexpected finding given that miRNAs usually act in trans, not in cis Robust repression of Fmr1 is conferred by combinations of Fx-mir miRNAs induced in Sertoli cells (SCs) during postnatal development when they terminate proliferation. Physiological significance is suggested by the finding that FMRP, the protein product of Fmr1, is downregulated when Fx-mir miRNAs are induced, and that FMRP loss causes SC hyperproliferation and spermatogenic defects. Fx-mir miRNAs not only regulate the expression of FMRP, but also regulate the expression of eIF4E and CYFIP1, which together with FMRP form a translational regulatory complex. Our results support a model in which Fx-mir family members act cooperatively to regulate the translation of batteries of mRNAs in a developmentally regulated manner in SCs

Molecular Determinants of Oocyte and Embryo Developmental Competence

The earliest stages of life, including the transition from the fully differentiated oocyte to the totipotent zygote, the first days of embryo cleavage and cell differentiation to form a blastocyst, and implantation of that blastocyst in the wall of the uterus, are somehow beautifully simple and strikingly complex at the same time. These stages, which represent the beginning of life for us and other vertebrates, are difficult to study, owing to a number of experimental and ethical considerations. However, advances in our understanding of nuclear reprogramming, transcriptional quiescence and activation, the maintenance of pluripotency, and what it takes for an embryo to initiate contact with the endometrium to generate a successful pregnancy, will without question have far-reaching influence for many scientific and medical disciplines. Here, I attempt to unravel some of these concepts, combining molecular and developmental biology with genome-wide analysis only recently made possible through advances in techniques with low input. These approaches, in combination, allow us to ask questions about early developmental systems that would not have been possible only years prior.In the oocyte, global transcriptional silencing is a highly conserved mechanism that is essential for the transition from the differentiated oocyte to the totipotent zygote. Here, I report that global transcriptional silencing in the mouse oocyte depends on an mRNA decay activator. By downregulating master regulators of transcription during oocyte growth, particularly a group of mRNAs encoding demethylases for H3K4 and H3K9, ZFP36L2 enables increased histone methylation that is associated with transcriptional silencing. These results uncover a mRNA decay mechanism that acts a developmental switch during growth of the mammalian oocyte, resulting in wide-spread shifts in chromatin modification, and mediating silencing of transcription in the oocyte.The pluripotent population of cells in the blastocyst, the inner cell mass, is established in the mouse embryo approximately three days after fertilization. These cells will undergo gastrulation to form the entire organism and can be maintained in culture as embryonic stem cells. I report here that UPF2, a mRNA decay activator, is needed specifically within the pluripotent inner cell mass of the mouse embryo for maintenance of pluripotency in the embryo in vivo, as well as for embryonic stem cells in vitro. That mRNA decay may underly the establishment or maintenance of this intriguing and complex population of cells, is an exciting possibility.Reproductive success depends on embryo implantation in the uterus, and in fertile and infertile couples alike, failure of the embryo to implant in the wall of the uterus accounts for up to 75% of all lost pregnancies. Here, I provide a qualitative assessment of gene expression and cellular communication networks within the major compartments of the human blastocyst that are most closely associated with successful implantation and ongoing pregnancy. Most strikingly, establishment and/or maintenance of the extraembryonic primitive endoderm lineage—following the second major embryonic differentiation event—most strongly differentiates embryos of high and low implantation potential. Unbiased machine learning identified genes within each embryo compartment most closely associated with implantation. Taken together, this data supports a model in which successful implantation and ongoing pregnancy predominantly depends upon the inner cell mass and highlights a potentially novel role for the extraembryonic primitive endoderm in early pregnancy success

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing