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Search Results for all work with filters:

  • Biology, Molecular

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Article

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

by Bo Yuan; Juanita Neira Fresneda; Davut Pehlivan; Teresa Santiago-Sim; Xiaofei Song; Jill Rosenfeld; Jennifer E. Posey; Vipulkumar Patel; Weihong Jin; Margaret P. Adam; Emma L. Baple; John Dean; Chin-To Fong; Scott E. Hickey; Louanne Hudgins; Eyby Leon; Suneeta Madan-Khetarpal; Lettie Rawlins; Cecilie F. Rustad; Asbjorg Stray-Pedersen; Kristian Tveten; Olivia Wenger; Jullianne Diaz; Laura Jenkins; Laura Martin; Marianne McGuire; Marguerite Pietryga; Linda Ramsdell; Leah Slattery; Farida Abid; Alison Bertuch; Dorothy Grange; LaDonna Immken; Christian P Schaaf; Hilde Van Esch; Weimin Bi; Sau Wai Cheung; Amy M. Breman; Janice L. Smith; Chad Shaw; Andrew H. Crosby; Christine Eng; Yaping Yang; James R. Lupski; Rui Xiao; Pengfei Liu

2019

Subjects
  • Biology, Genetics
  • Biology, Molecular
  • File Download
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Abstract:Close

Purpose: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. Methods: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. Results: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. Conclusion: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

Article

Natural and Synthetic Sialylated Glycan Microarrays and Their Applications

by Alyssa M. McQuillan; Lauren Byrd-Leotis; Jamie Heimburg-Molinaro; Richard Cummings

2019

Subjects
  • Biology, Molecular
  • Health Sciences, Immunology
  • Chemistry, Biochemistry
  • File Download
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Abstract:Close

This focused chapter serves as a short survey of glycan microarrays that are available with sialylated glycans, including both defined and shotgun arrays, their generation, and their utility in studying differential binding interactions to sialylated compounds, highlighting N-glycolyl (Gc) modified sialylated compounds. A brief discussion of binding interactions by lectins, antibodies, and viruses, and their relevance that have been observed with sialylated glycan microarrays is presented, as well as a discussion of cross-comparisons of array platforms and efforts to centralize and standardize the glycan microarray data.

Article

Calcineurin: A poorly understood regulator of muscle mass

by Matthew B. Hudson; Russ Price

2013

Subjects
  • Health Sciences, Medicine and Surgery
  • Biology, Molecular
  • File Download
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Abstract:Close

This review will discuss the existing literature that has examined the role of calcineurin (CnA) in the regulation of skeletal muscle mass in conditions associated with hypertrophic growth or atrophy. Muscle mass is determined by the balance between protein synthesis and degradation which is controlled by a number of intracellular signaling pathways, most notably the insulin/IGF/phosphatidylinositol 3-kinase (PI3K)/Akt system. Despite being activated by IGF-1 and having well-described functions in the determination of muscle fiber phenotypes, calcineurin (CnA), a Ca2+-activated serine/threonine phosphatase, and its downstream signaling partners have garnered little attention as a regulator of muscle mass. Compared to other signaling pathways, the relatively few studies that have examined the role of CnA in the regulation of muscle size have produced discordant results. The reasons for these differences is not obvious but may be due to the selective nature of the genetic models studied, fluctuations in the endogenous level of CnA activity in various muscles, and the variable use of CnA inhibitors to inhibit CnA signaling. Despite the inconsistent nature of the outcomes, there is sufficient direct and indirect evidence to conclude that CnA plays a role in the regulation of skeletal muscle mass. This article is part of a Directed Issue entitled: Molecular basis of muscle wasting.

Article

Insulin increases the functional activity of the renal NaCl cotransporter

by Maria Chavez-Canales; Juan Pablo Arroyo; Benjamin Ko; Norma Vazquez; Rocio Bautista; Maria Castaneda-Bueno; Norma A. Bobadilla; Robert S. Hoover Jr; Gerardo Gamba

2013

Subjects
  • Health Sciences, Medicine and Surgery
  • Biology, Physiology
  • Biology, Molecular
  • File Download
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Abstract:Close

Objectives: Insulin is recognized to increase renal salt reabsorption in the distal nephron and hyperinsulinemic states have been shown to be associated with increased expression of the renal NaCl cotransporter (NCC). However, the effect of insulin on NCC functional activity has not been reported. Methods: Using a heterologous expression system of Xenopus laevis oocytes, a mouse distal convoluted cell line, mDCT15 cells, endogenously expressing NCC, and an ex-vivo kidney perfusion technique, we assessed the effect of insulin on the activity and phosphorylation of NCC. The signaling pathway involved was analyzed. Results: In Xenopus oocytes insulin increases the activity of NCC together with its phosphorylation at threonine residue 58. Activation of NCC by insulin was also observed in mDCT15 cells. Additionally, insulin increased the NCC phosphorylation in kidney under the ex-vivo perfusion technique. In oocytes and mDCT15 cells, insulin effect on NCC was prevented with inhibitors of phosphatidylinositol 3-kinase (PI3K), mTORC2, and AKT1 kinases, but not by inhibitors of MAP or mTORC1 kinases, suggesting that PI3K-mTORC2-AKT1 is the intracellular pathway required. Additionally, activation of NCC by insulin was not affected by wild-type or mutant versions of with no lysine kinase 1, with no lysine kinase 4, or serum glucocorticoid kinase 1, but it was no longer observed in the presence of wild-type or the dominant negative, catalytically inactive with no lysine kinase 3, implicating this kinase in the process. Conclusion: Insulin induces activation and phosphorylation of NCC. This effect could play an important role in arterial hypertension associated with hyperinsulinemic states, such as obesity, metabolic syndrome, or type 2 diabetes mellitus.

Article

Inhibition of IκB Kinase-Nuclear Factor-κB Signaling Pathway by 3,5-Bis(2-flurobenzylidene)piperidin-4-one (EF24), a Novel Monoketone Analog of Curcumin

by Andrea L. Kasinski; Yuhong Du; Shala L. Thomas; Jing Zhao; Shi-Yong Sun; Fadlo Khuri; Cun-Yu Wang; Mamoru Shoji; Aiming Sun; James P Snyder; Dennis C Liotta; Haian Fu

2008

Subjects
  • Biology, Molecular
  • Health Sciences, Pharmacology
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The nuclear factor-κB (NF-κB) signaling pathway has been targeted for therapeutic applications in a variety of human diseases, includuing cancer. Many naturally occurring substances, including curcumin, have been investigated for their actions on the NF-κB pathway because of their significant therapeutic potential and safety profile. A synthetic monoketone compound termed 3,5-bis(2-flurobenzylidene)piperidin-4-one (EF24) was developed from curcumin and exhibited potent anticancer activity. Here, we report a mechanism by which EF24 potently suppresses the NF-κB signaling pathway through direct action on IκB kinase (IKK). We demonstrate that 1) EF24 induces death of lung, breast, ovarian, and cervical cancer cells, with a potency about 10 times higher than that of curcumin; 2) EF24 rapidly blocks the nuclear translocation of NF-κB, with an IC50 value of 1.3 μM compared with curcumin, with an IC50 value of 13 μM; 3) EF24 effectively inhibits tumor necrosis factor (TNF)-α-induced IκB phosphorylation and degradation, suggesting a role of this compound in targeting IKK; and 4) EF24 indeed directly inhibits the catalytic activity of IKK in an in vitro-reconstituted system. Our study identifies IKK as an effective target for EF24 and provides a molecular explanation for a superior activity of EF24 over curcumin. The effective inhibition of TNF-α-induced NF-κB signaling by EF24 extends the therapeutic application of EF24 to other NF-κB-dependent diseases, including inflammatory diseases such as rheumatoid arthritis.

Article

Fyn Regulates Adipogenesis by Promoting PIKE-A/STAT5a Interaction

by Margaret Chui Ling Tse; Xia Liu; Seran Yang; Keqiang Ye; Chi Bun Chan

2013

Subjects
  • Health Sciences, Pathology
  • Biology, Molecular
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Fyn is a tyrosine kinase with multiple roles in a variety of cellular processes. Here we report that Fyn is a new kinase involved in adipocyte differentiation. Elevated Fyn protein is detected specifically in the adipocytes of obese mice. Moreover, Fyn expression increases progressively in 3T3-L1 cells during in vitro adipogenesis, which correlates with its kinase activity. Inhibition of Fyn by either genetic or pharmacological manipulation restrains the 3T3-L1 preadipocytes from fully differentiating into mature adipocytes. Mechanistically, Fyn regulates the activity of the adipogenic transcription factor signal transducer and activator of transcription 5a (STAT5a) through enhancing its interaction with the GTPase phosphoinositide 3-kinase enhancer A (PIKE-A). The STAT5a activity is therefore reduced in Fyn- or PIKE-ablated adipose tissues, leading to diminished expression of adipogenic markers and adipocyte differentiation. Our data thus demonstrate a novel functional interaction between Fyn, PIKE-A, and STAT5a in mediating adipogenesis.

Article

ZNF121 interacts with ZBRK1 and BRCA1 to regulate their target genes in mammary epithelial cells

by Ang Luo; Kailun Zhang; Yanxia Zhao; Zhengmao Zhu; Liya Fu; Jin-Tang Dong

2018

Subjects
  • Chemistry, Biochemistry
  • Biology, Genetics
  • Biology, Molecular
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The novel zinc finger protein 121 (ZNF121) has been demonstrated to physically and functionally associate with the MYC oncoprotein to regulate cell proliferation and likely breast cancer development. To further understand how ZNF121 functions in cell proliferation and carcinogenesis, we identified and characterized the interaction of ZNF121 with zinc finger and BRCA1-interacting protein with a KRAB domain 1 (ZBRK1), a breast and ovarian cancer susceptibility protein 1 (BRCA1)-interacting protein, using the yeast two-hybrid assay and other approaches. We also found that ZNF121 bound to BRCA1. Functionally, ZFN121 suppressed the expression of ANG1 and HMGA2, two common downstream targets of ZBRK1 and BRCA1. Interestingly, ZNF121 also regulated the expression of BRCA1 and ZBRK1. These findings suggest that ZNF121 is likely a member of the BRCA1/CtIP/ZBRK1 repressor complex that plays a role in breast cancer.

Article

Analysis of Ribonucleotide 5 '-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays

by Gaofei Lu; Gregory Bluemling; Paul Collop; Michael Hager; Damien Kuiper; Bharat P. Gurale; George Painter; Abel De La Rosa; Alexander A. Kolykhalov

2017

Subjects
  • Biology, Molecular
  • Biology, Virology
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Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primertemplate pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn 2+ is required for enzymatic activity, while Mg 2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5′-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2′-C-methyl- and 2′-C-ethynyl-substituted analog 5′-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.

Article

Zebularine: A Novel DNA Methylation Inhibitor that Forms a Covalent Complex with DNA Methyltransferases

by Lei Zhou; Xiaodong Cheng; B.A. Connolly; M.J. Dickman; P.J. Hurd; D.P. Hornby

2002

Subjects
  • Chemistry, Biochemistry
  • Biology, Molecular
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Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC) provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus haemolyticus (M.Hha I) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an analogue often referred to as zebularine and known to give rise to high-affinity complexes with MTases. X-ray crystallography has demonstrated the formation of a covalent bond between M.Hha I and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism of action of the anti-cancer drug zebularine.

Article

The Drosophila Helicase Maleless (MLE) is Implicated in Functions Distinct From its Role in Dosage Compensation

by Simona Cugusi; Satish Kallappagoudar; Huiping Ling; John Lucchesi

2015

Subjects
  • Biology, Molecular
  • Chemistry, Biochemistry
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Helicases are ubiquitous enzymes that unwind or remodel single or double-stranded nucleic acids, and that participate in a vast array of metabolic pathways. The ATP-dependent DEXH-box RNA/DNA helicase MLE was first identified as a core member of the chromatin remodeling MSL complex, responsible for dosage compensation in Drosophila males. Although this complex does not assemble in females, MLE is present. Given the multiplicity of functions attributed to its mammalian ortholog RNA helicase A, we have carried out an analysis for the purpose of determining whether MLE displays the same diversity. We have identified a number of different proteins that associate with MLE, implicating its role in specific pathways. We have documented this association in selected examples that include the spliceosome complex, heterogeneous Nuclear Ribonucleoproteins involved in RNA Processing and in Heterochromatin Protein 1 deposition, and the NuRD complex.
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