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Zhang P
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SeqTailor: a user-friendly webserver for the extraction of DNA or (opens in new window)

NUCLEIC ACIDS RESEARCH 2019 JUL 2; 47(W1):W623-W631
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Human whole-genome-sequencing reveals about 4 000 000 genomic variants
Dunn A, Reed B, Erazo J, Ben-Ezra A, Kreek MJ
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Signaling properties of structurally diverse kappa opioid receptor ligands: towards in vitro models of in vivo responses

ACS CHEMICAL NEUROSCIENCE
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Biased ligands preferentially activate certain signaling pathways downstream of their target receptor, leading to differential physiological or behavioral responses downstream. The kappa opioid receptor (KOR) is a drug target for diseases involving mood and reward, such as depression and addiction. Biased KOR ligands offer the potential to overcome negative side effects that have previously hampered the therapeutic development of KOR agonists by preferentially activating certain signaling pathways. Understanding relationships between ligand bias and behavior is difficult, however, because differences in cellular context and bias quantification methods lead to variation between studies. Here, a set of 21 structurally diverse KOR ligands were tested in parallel, to systematically quantify ligand bias at the KOR. Compounds included the endogenous peptide ligand Dynorphin A(1-17), two novel compounds synthesized for our research, and 18 additional compounds of different structural classes, including morphinans and the natural product Salvinorin A. Compounds were tested for their activity in early KOR signaling pathways (G-protein and β-arrestin recruitment) in KOR-expressing U2OS cells, and ligand bias was calculated. A subset of compounds was tested for sedative properties in the rotarod assay in mice. We found that rotarod sedation significantly correlated with β-arrestin signaling in this system, indicating that this in vitro system can be used to accurately describe this in vivo behavior caused by KOR agonists. Additionally, downstream signaling pathways ERK1/2 and mTOR were evaluated, and we determined that signaling via both of these pathways could diverge from KOR-mediated G-protein and arrestin signaling in this system.
Le Moene O, Stavarache M, Ogawa S, Musatov S, Agmo A
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Estrogen receptors alpha and beta in the central amygdala and the ventromedial nucleus of the hypothalamus: Sociosexual behaviors, fear and arousal in female rats during emotionally challenging events (opens in new window)

BEHAVIOURAL BRAIN RESEARCH 2019 JUL; 367(?):128-142
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Estrogens receptors (ER) are involved in several sociosexual behaviors and fear responses. In particular, the ER alpha is important for sexual behaviors, whereas ER beta modulates anxiolytic responses. Using shRNA directed either against the ER alpha or the ER beta RNAs (or containing luciferase control) encoded within an adeno-associated viral vector, we silenced these receptors in the ventromedial nucleus of the hypothalamus (VMN) and the central amygdala (CeA). We exposed ovariectomized female rats, sequentially treated with estradiol benzoate and progesterone, to five stimuli, previously reported to elicit positive and negative affect. The subjects were housed in groups of 4 females and 3 males in a seminatural environment for several days before hormone treatment. We analyzed the frequency of a large number of behavior patterns. In addition, we performed analyses of co-occurrence in order to detect changes in the structure of behavior after infusion of the vectors. Silencing the ER alpha in the VMN disrupted lordosis and showed some anxiolytic properties in aversive situations, whereas silencing of the ER beta in this structure had no effect. This was also the case after silencing the ER alpha in the CeA. Silencing of the ER beta in this structure increased risk assessment, an expression of anxiety, and increased olfactory exploration of the environment. We hypothesize that the ER beta in the CeA has an important role in the well-established anxiolytic effects of estrogens, and that it may modulate arousal level. Furthermore, it seems that the ER alpha in the VMN is anxiogenic in aversive or threatening situations, in agreement with other studies.
Igoshin OA
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Biophysics at the coffee shop: lessons learned working with George Oster (opens in new window)

MOLECULAR BIOLOGY OF THE CELL 2019 JUL 22; 30(16):1882-1889
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Over the past 50 years, the use of mathematical models, derived from
Imai-Okazaki A
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Heterozygosity mapping for human dominant trait variants (opens in new window)

HUMAN MUTATION 2019 JUL; 40(7):996-1004
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Homozygosity mapping is a well-known technique to identify runs of
Weber E, Buzovetsky O, Heston L, Yu KP, Knecht KM, El-Guindy A, Miller G, Xiong Y
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A Noncanonical Basic Motif of Epstein-Barr Virus ZEBRA Protein Facilitates Recognition of Methylated DNA, High-Affinity DNA Binding, and Lytic Activation (opens in new window)

JOURNAL OF VIROLOGY 2019 JUL; 93(14):? Article e00724-19
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The pathogenesis of Epstein-Barr virus (EBV) infection, including development of lymphomas and carcinomas, is dependent on the ability of the virus to transit from latency to the lytic phase. This conversion, and ultimately disease development, depends on the molecular switch protein, ZEBRA, a viral bZIP transcription factor that initiates transcription from promoters of viral lytic genes. By binding to the origin of viral replication, ZEBRA is also an essential replication protein. Here, we identified a novel DNA-binding motif of ZEBRA, N terminal to the canonical bZIP domain. This RRTRK motif is important for high-affinity binding to DNA and is essential for recognizing the methylation state of viral promoters. Mutations in this motif lead to deficiencies in DNA binding, recognition of DNA methylation, lytic cycle DNA replication, and viral late gene expression. This work advances our understanding of ZEBRA-dependent activation of the viral lytic cascade. IMPORTANCE The binding of ZEBRA to methylated and unmethylated viral DNA triggers activation of the EBV lytic cycle, leading to viral replication and, in some patients, cancer development. Our work thoroughly examines how ZEBRA uses a previously unrecognized basic motif to bind nonmethylated and methylated DNA targets, leading to viral lytic activation. Our findings show that two different positively charged motifs, including the canonical BZIP domain and a newly identified RRTRK motif, contribute to the mechanism of DNA recognition by a viral AP-1 protein. This work contributes to the assessment of ZEBRA as a potential therapeutic target for antiviral and oncolytic treatments.
Lapointe T
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Effects of combined escitalopram and aripiprazole in rats: role of the (opens in new window)

PSYCHOPHARMACOLOGY 2019 JUL; 236(7):2283-2283
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After publication of this paper, the authors determined an error in
Schneeberger M, Parolari L, Das Banerjee T, Bhave V, Wang P, Patel B, Topilko T, Wu Z, Choi CHJ, Yu X, Pellegrino K, Engel EA, Cohen P, Renier N, Friedman JM, Nectow AR
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Regulation of Energy Expenditure by Brainstem GABA Neurons (opens in new window)

CELL 2019 JUL 25; 178(3):672-685.e12
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Homeostatic control of core body temperature is essential for survival. Temperature is sensed by specific neurons, in turn eliciting both behavioral (i.e., locomotion) and physiologic (i.e., thermogenesis, vasodilatation) responses. Here, we report that a population of GABAergic (Vgat-expressing) neurons in the dorsolateral portion of the dorsal raphe nucleus (DRN), hereafter DRNVgat neurons, are activated by ambient heat and bidirectionally regulate energy expenditure through changes in both thermogenesis and locomotion. We find that DRNVgat neurons innervate brown fat via a descending projection to the raphe pallidus (RPa). These neurons also densely innervate ascending targets implicated in the central regulation of energy expenditure, including the hypothalamus and extended amygdala. Optogenetic stimulation of different projection targets reveals that DRNVgat neurons are capable of regulating thermogenesis through both a "direct" descending pathway through the RPa and multiple "indirect" ascending pathways. This work establishes a key regulatory role for DRNVgat neurons in controlling energy expenditure.
Farfara D, Feierman E, Richards A, Revenko AS, MacLeod RA, Norris EH, Strickland S
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Knockdown of circulating C1 inhibitor induces neurovascular impairment, glial cell activation, neuroinflammation, and behavioral deficits (opens in new window)

GLIA 2019 JUL; 67(7):1359-1373
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The cross-talk between blood proteins, immune cells, and brain function involves complex mechanisms. Plasma protein C1 inhibitor (C1INH) is an inhibitor of vascular inflammation that is induced by activation of the kallikrein-kinin system (KKS) and the complement system. Knockout of C1INH was previously correlated with peripheral vascular permeability via the bradykinin pathway, yet there was no evidence of its correlation with blood-brain barrier (BBB) integrity and brain function. In order to understand the effect of plasma C1INH on brain pathology via the vascular system, we knocked down circulating C1INH in wild-type (WT) mice using an antisense oligonucleotide (ASO), without affecting C1INH expression in peripheral immune cells or the brain, and examined brain pathology. Long-term elimination of endogenous C1INH in the plasma induced the activation of the KKS and peritoneal macrophages but did not activate the complement system. Bradykinin pathway proteins were elevated in the periphery and the brain, resulting in hypotension. BBB permeability, extravasation of plasma proteins into the brain parenchyma, activation of glial cells, and elevation of pro-inflammatory response mediators were detected. Furthermore, infiltrating innate immune cells were observed entering the brain through the lateral ventricle walls and the neurovascular unit. Mice showed normal locomotion function, yet cognition was impaired and depressive-like behavior was evident. In conclusion, our results highlight the important role of regulated plasma C1INH as it acts as a gatekeeper to the brain via the neurovascular system. Thus, manipulation of C1INH in neurovascular disorders might be therapeutically beneficial.
Marrocco J, Gray JD, Kogan JF, Einhorn NR, O'Cinneide EM, Rubin TG, Carroll TS, Schmidt EF, McEwen BS
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Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood (opens in new window)

FRONTIERS IN BEHAVIORAL NEUROSCIENCE 2019 JUL 11; 13(?):? Article 157
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Early life experiences program brain structure and function and contribute to behavioral endophenotypes in adulthood. Epigenetic control of gene expression by those experiences affect discrete brain regions involved in mood, cognitive function and regulation of hypothalamic-pituitary-adrenal (HPA) axis. In rodents, acute restraint stress increases the expression of the repressive histone H3 lysine 9 tri-methylation (H3K9me3) in hippocampal fields, including the CA3 pyramidal neurons. These CA3 neurons are crucially involved in cognitive function and mood regulation as well as activation of glucocorticoid (CORT) secretion. CA3 neurons also exhibit structural and functional changes after early-life stress (ELS) as well as after chronic stress in adulthood. Using a protocol of chronic ELS induced by limited bedding and nesting material followed by acute-swim stress (AS) in adulthood, we show that mice with a history of ELS display a blunted CORT response to AS, despite exhibiting activation of immediate early genes after stress similar to that found in control mice. We find that ELS induced persistently increased expression of the repressive H3K9me3 histone mark in the CA3 subfield at baseline that was subsequently decreased following AS. In contrast, AS induced a transient increase of this mark in control mice. Using translating ribosome affinity purification (TRAP) method to isolate CA3 translating mRNAs, we found that expression of genes of the epigenetic gene family, GABA/glutamate family, and glucocorticoid receptors binding genes were decreased transiently in control mice by AS and showed a persistent reduction in ELS mice. In most cases, AS in ELS mice did not induce gene expression changes. A stringent filtering of genes affected by AS in control and ELS mice revealed a noteworthy decrease in gene expression change in ELS mice compared to control. Only 18 genes were selectively regulated by AS in ELS mice and encompassed pathways such as circadian rhythm, inflammatory response, opioid receptors, and more genes included in the glucocorticoid receptor binding family. Thus, ELS programs a restricted translational response to stress in stress-sensitive CA3 neurons leading to persistent changes in gene expression, some of which mimic the transient effects of AS in control mice, while leaving in operation the immediate early gene response to AS.