Note on the Measures of Dependence in Terms of Copulas

AbstractThe dependence structure among each risk factors has been an important topic for researches both from theoretical and applied standpoints. To measure such dependence, several characteristic quantities have been already introduced and widely employed, which include, for instance, the population version of Kendall's tau (τ) and/or Spearman's rho (ρ). Copulas, on the other hand, are well known tools for understanding the dependence relation among random variables, and the above τ and ρ are expressed in terms of copulas. In this note, we generalize these expressions. We also compute the extended formula for the Archimedean copulas as well as its generalized copulas, and pursue the possibility of its applications

MOLECULAR MECHANISMS IN THE DEVELOPING AND MATURING BRAIN

Neurons, unlike other cell types, persist throughout the entire lifespan of an organism. Additionally, neurons use multiple anti-apoptotic brakes during different stages of their life cycle in order to maintain their long-term survival. This dissertation investigates the role of two well-known anti-apoptotic genes, Bcl-xL and miR-29, which are believed to serve important functions in preventing cell death during embryonic brain development and during the period of postnatal brain maturation, respectively. Using conditional knockout mouse models of Bcl-xL and miR-29, I found that these genes may have additional non-apoptotic roles at different timepoints during the neuron’s life cycle, challenging the previously accepted roles of these genes. First, I found that Bcl-xL, which is believed to be critical for brain development during the embryonic stages, was expressed at low levels in the rapidly dividing neuronal progenitor cells and was thus dispensable for the survival of these cells during embryonic development. In contrast, the early differentiated postmitotic neurons acutely rely on Bcl-xL for their survival, the lack of which results in severe consequences in mice including microcephaly and neurobehavioral deficits such as hyperactivity, increased risk-taking and self-injurious behaviors. Second, to probe the role of miR-29, a microRNA that is known to be critical for neuronal maturation by preventing apoptosis in neurons, I generated knockout mice that were conditionally deleted for miR-29. We and other labs have predicted that the main role of miR-29 is to prevent apoptosis and that deleting miR-29 could lead to widespread neuronal death. Surprisingly, however, miR-29-deficient mice exhibit no signs of cell death in the brain. In contrast, we identified a novel function of miR-29 in governing DNA methylation, an event that has been primarily studied in the context of cancer and whose roles in the brain are just beginning to be uncovered. I have found that miR-29 has an important epigenetic role in the brain via its ability to target the 3’ untranslated region (3’UTR) of a key DNA methyltransferase known as Dnmt3a. miR-29-deleted brains have increased levels of Dnmt3a, resulting in widespread hypermethylation across the genome. This, in turn, leads to transcriptional repression of multiple neuronal genes in the miR-29 knockout brains, resulting in severe neurobehavioral deficits including hyperactivity, hypersociability, excessive self-grooming and repetitive behaviors. Lastly, using RNAseq and gene association studies, I found that the pathways that are dysregulated in the miR-29-deleted mice are similar to those that are disrupted in the brains of patients with autism spectrum disorder (ASD), suggesting that miR-29 could be tested as a potential therapy in neurodevelopmental disorders in the future.Doctor of Philosoph

Is the Comet Assay a Sensitive Procedure for Detecting Genotoxicity?

Although the Comet assay, a procedure for quantitating DNA damage in mammalian cells, is considered sensitive, it has never been ascertained that its sensitivity is higher than the sensitivity of other genotoxicity assays in mammalian cells. To determine whether the power of the Comet assay to detect a low level of genotoxic potential is superior to those of other genotoxicity assays in mammalian cells, we compared the results of Comet assay with those of micronucleus test (MN test). WTK1 human lymphoblastoid cells were exposed to methyl nitrosourea (MNU), ethyl nitrosourea (ENU), methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS), bleomycin (BLM), or UVC. In Comet assay, cells were exposed to each mutagen with (Comet assay/araC) and without (Comet assay) DNA repair inhibitors (araC and hydroxyurea). Furthermore, acellular Comet assay (acellular assay) was performed to determine how single-strand breaks (SSBs) as the initial damage contributes to DNA migration and/or to micronucleus formation. The lowest genotoxic dose (LGD), which is defined as the lowest dose at which each mutagen causes a positive response on each genotoxicity assay, was used to compare the power of the Comet assay to detect a low level of genotoxic potential and that of MN test; that is, a low LGD indicates a high power. Results are summarized as follows: (1) for all mutagens studied, LGDs were MN test ≦ Comet assay; (2) except for BLM, LGDs were Comet assay/araC ≦ MN test; (3) except for UVC and MNU, LGDs were acellular assay ≦ Comet assay/araC ≦ MN test ≦ Comet assay. The following is suggested by the present findings: (1) LGD in the Comet assay is higher than that in MN test, which suggests that the power of the MN test to detect a low level of genotoxic potential is superior to that of the Comet assay; (2) for the studied mutagens, all assays were able to detect all mutagens correctly, which suggests that the sensitivity of the Comet assay and that of the MN test were exactly identical; (3) the power of the Comet assay to detect a low level of genotoxic potential can be elevated to a level higher than that of MN test by using DNA resynthesis inhibitors, such as araC and HU

Fluctuated spin-orbital texture of Rashba-split surface states in real and reciprocal space

Spin-orbit interaction (SOI) in low-dimensional systems, namely Rashba systems and the edge states of topological materials, is extensively studied in this decade as a promising source to realize various fascinating spintronic phenomena, such as the source of the spin current and spin-mediated energy conversion. Here, we show the odd fluctuation in the spin-orbital texture in a surface Rashba system on Bi/InAs(110)-(2$\times$1) by spin- and angle-resolved photoelectron spectroscopy and a numerical simulation based on a density-functional theory (DFT) calculation. The surface state shows a paired parabolic dispersion with the spin degeneracy lifted by the Rashba effect. Although its spin polarization should be fixed in a particular direction based on the Rashba model, the observed spin polarization varies greatly and even reverses its sign depending on the wavenumber. DFT calculations also reveal that the spin directions of two inequivalent Bi chains on the surface change from nearly parallel (canted-parallel) to anti-parallel in real space in the corresponding wavevector region. These results point out an oversimplification of the nature of spin in Rashba and Dirac systems and provide more freedom than expected for spin manipulation of photoelectrons.Comment: 23 pages, 7 figure

Mature neurons dynamically restrict apoptosis via redundant premitochondrial brakes

Apoptotic cell death is critical for the early development of the nervous system, but once the nervous system is established, the apoptotic pathway becomes highly restricted in mature neurons. However, the mechanisms underlying this increased resistance to apoptosis in these mature neurons are not completely understood. We have previously found that members of the miR-29 family of microRNAs (miRNAs) are induced with neuronal maturation and that overexpression of miR-29 was sufficient to restrict apoptosis in neurons. To determine whether endogenous miR-29 alone was responsible for the inhibition of cytochrome c release in mature neurons, we examined the status of the apoptotic pathway in sympathetic neurons deficient for all three miR-29 family members. Unexpectedly, we found that the apoptotic pathway remained largely restricted in miR-29-deficient mature neurons. We therefore probed for additional mechanisms by which mature neurons resist apoptosis. We identify miR-24 as another miRNA that is upregulated in the maturing cerebellum and sympathetic neurons that can act redundantly with miR-29 by targeting a similar repertoire of pro-death BH3-only genes. These results reveal that mature neurons engage redundant brakes to restrict the apoptotic pathway and ensure their long-term survival

Phenethyl iosothiocyanate activates leptin signaling

Obesity, a principal risk factor for the development of diabetes mellitus, heart disease, and hypertension, is a growing and serious health problem all over the world. Leptin is a weight-reducing hormone produced by adipose tissue, which decreases food intake via hypothalamic leptin receptors (Ob-Rb) and the Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) signaling pathway. Protein tyrosine phosphatase 1B (PTP1B) negatively regulates leptin signaling by dephosphorylating JAK2, and the increased activity of PTP1B is implicated in the pathogenesis of obesity. Hence, inhibition of PTP1B may help prevent and reduce obesity. In this study, we revealed that phenethyl isothiocyanate (PEITC), a naturally occurring isothiocyanate in certain cruciferous vegetables, potently inhibits recombinant PTP1B by binding to the reactive cysteinyl thiol. Moreover, we found that PEITC causes the ligand-independent phosphorylation of Ob-Rb, JAK2, and STAT3 by inhibiting cellular PTP1B in differentiated human SH-SY5Y neuronal cells. PEITC treatment also induced nuclear accumulation of phosphorylated STAT3, resulting in enhanced anorexigenic POMC expression and suppressed orexigenic NPY/AGRP expression. We demonstrated that oral administration of PEITC to mice significantly reduces food intake, and stimulates hypothalamic leptin signaling. Our results suggest that PEITC might help prevent and improve obesity

Glycolate is a Novel Marker of Vitamin B2 Deficiency Involved in Gut Microbe Metabolism in Mice

Microbes in the human gut play a role in the production of bioactive compounds, including some vitamins. Although several studies attempted to identify definitive markers for certain vitamin deficiencies, the role of gut microbiota in these deficiencies is unclear. To investigate the role of gut microbiota in deficiencies of four vitamins, B2, B6, folate, and B12, we conducted a comprehensive analysis of metabolites in mice treated and untreated with antibiotics. We identified glycolate (GA) as a novel marker of vitamin B2 (VB2) deficiency, and show that gut microbiota sense dietary VB2 deficiency and accumulate GA in response. The plasma GA concentration responded to reduced VB2 supply from both the gut microbiota and the diet. These results suggest that GA is a novel marker that can be used to assess whether or not the net supply of VB2 from dietary sources and gut microbiota is sufficient. We also found that gut microbiota can provide short-term compensation for host VB2 deficiency when dietary VB2 is withheld

Bcl-xL Is Essential for the Survival and Function of Differentiated Neurons in the Cortex That Control Complex Behaviors

Apoptosis plays an essential role during brain development, yet the precise mechanism by which this pathway is regulated in the brain remains unknown. In particular, mammalian cells are known to express multiple anti-apoptotic Bcl-2 family proteins. However, the cells of the developing brain could also exist in a primed state in which the loss of a single anti-apoptotic Bcl-2 family protein is sufficient to trigger apoptosis. Here, we examined the critical role of Bcl-xL, an anti-apoptotic protein, during brain development. Using conditional knock-out mice in which Bcl-xL is deleted in neural progenitor cells (Bcl-xLEmx1–Cre), we show that the loss of Bcl-xL is not sufficient to trigger apoptosis in these proliferating progenitors. In contrast, specific populations of postmitotic neurons derived from these progenitors, including upper layer cortical neurons and the CA1–CA3 regions of the hippocampus, were acutely dependent on Bcl-xL. Consistent with this finding, deletion of Bcl-xL selectively in the postmitotic neurons in the brain (Bcl-xLNex–Cre) also resulted in similar patterns of apoptosis. This Bcl-xL deficiency-induced neuronal death was a consequence of activation of the apoptotic pathway, because the cell death was rescued with codeletion of the proapoptotic proteins Bax and Bak. Importantly, the loss of these Bcl-xL-dependent neurons led to severe neurobehavioral abnormalities, including deficits in motor learning, hyperactivity, and increased risk-taking and self-injurious behaviors. Together, our results identify a population of neurons in the developing brain that are acutely dependent on Bcl-xL during the peak period of synaptic connectivity that are important for the establishment of higher-order complex behaviors