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Updated: 16 weeks 2 days ago

Identification of DNA primase inhibitors via a combined fragment-based and virtual screening.

Fri, 11/04/2016 - 5:17am

Identification of DNA primase inhibitors via a combined fragment-based and virtual screening.

Sci Rep. 2016 Nov 02;6:36322

Authors: Ilic S, Akabayov SR, Arthanari H, Wagner G, Richardson CC, Akabayov B

Abstract
The structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.

PMID: 27805033 [PubMed - in process]

Selvamicin, an atypical antifungal polyene from two alternative genomic contexts.

Fri, 11/04/2016 - 5:17am
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Selvamicin, an atypical antifungal polyene from two alternative genomic contexts.

Proc Natl Acad Sci U S A. 2016 Nov 1;:

Authors: Van Arnam EB, Ruzzini AC, Sit CS, Horn H, Pinto-Tomás AA, Currie CR, Clardy J

Abstract
The bacteria harbored by fungus-growing ants produce a variety of small molecules that help maintain a complex multilateral symbiosis. In a survey of antifungal compounds from these bacteria, we discovered selvamicin, an unusual antifungal polyene macrolide, in bacterial isolates from two neighboring ant nests. Selvamicin resembles the clinically important antifungals nystatin A1 and amphotericin B, but it has several distinctive structural features: a noncationic 6-deoxymannose sugar at the canonical glycosylation site and a second sugar, an unusual 4-O-methyldigitoxose, at the opposite end of selvamicin's shortened polyene macrolide. It also lacks some of the pharmacokinetic liabilities of the clinical agents and appears to have a different target. Whole genome sequencing revealed the putative type I polyketide gene cluster responsible for selvamicin's biosynthesis including a subcluster of genes consistent with selvamicin's 4-O-methyldigitoxose sugar. Although the selvamicin biosynthetic cluster is virtually identical in both bacterial producers, in one it is on the chromosome, in the other it is on a plasmid. These alternative genomic contexts illustrate the biosynthetic gene cluster mobility that underlies the diversity and distribution of chemical defenses by the specialized bacteria in this multilateral symbiosis.

PMID: 27803316 [PubMed - as supplied by publisher]

Structural elements of an NRPS cyclization domain and its intermodule docking domain.

Fri, 11/04/2016 - 5:17am
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Structural elements of an NRPS cyclization domain and its intermodule docking domain.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12432-12437

Authors: Dowling DP, Kung Y, Croft AK, Taghizadeh K, Kelly WL, Walsh CT, Drennan CL

Abstract
Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA-F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and l-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes l-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-Å resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-Å-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct.

PMID: 27791103 [PubMed - in process]

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Thu, 11/03/2016 - 3:52am
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Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Nat Genet. 2016 Oct 31;:

Authors: Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A, BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC, LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC

Abstract
The genetic architecture of human reproductive behavior-age at first birth (AFB) and number of children ever born (NEB)-has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.

PMID: 27798627 [PubMed - as supplied by publisher]

Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function.

Thu, 11/03/2016 - 3:52am
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Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function.

MBio. 2016 Oct 18;7(5):

Authors: Simpson BW, Owens TW, Orabella MJ, Davis RM, May JM, Trauger SA, Kahne D, Ruiz N

Abstract
The surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS), creating a permeability barrier against toxic molecules, including many antimicrobials. To assemble LPS on their surface, Gram-negative bacteria must extract newly synthesized LPS from the inner membrane, transport it across the aqueous periplasm, and translocate it across the outer membrane. The LptA to -G proteins assemble into a transenvelope complex that transports LPS from the inner membrane to the cell surface. The Lpt system powers LPS transport from the inner membrane by using a poorly characterized ATP-binding cassette system composed of the ATPase LptB and the transmembrane domains LptFG. Here, we characterize a cluster of residues in the groove region of LptB that is important for controlling LPS transport. We also provide the first functional characterization of LptFG and identify their coupling helices that interact with the LptB groove. Substitutions at conserved residues in these coupling helices compromise both the assembly and function of the LptB2FG complex. Defects in LPS transport conferred by alterations in the LptFG coupling helices can be rescued by changing a residue in LptB that is adjacent to functionally important residues in the groove region. This suppression is achieved by increasing the ATPase activity of the LptB2FG complex. Taken together, these data identify a specific binding site in LptB for the coupling helices of LptFG that is responsible for coupling of ATP hydrolysis by LptB with LptFG function to achieve LPS extraction.
IMPORTANCE: Lipopolysaccharide (LPS) is synthesized at the cytoplasmic membrane of Gram-negative bacteria and transported across several compartments to the cell surface, where it forms a barrier that protects these organisms from antibiotics. The LptB2FG proteins form an ATP-binding cassette (ABC) transporter that uses energy from ATP hydrolysis in the cytoplasm to facilitate extraction of LPS from the outer face of the cytoplasmic membrane prior to transport to the cell surface. How ATP hydrolysis is coupled with LPS release from the membrane is not understood. We have identified residues at the interface between the ATPase and the transmembrane domains of this heteromeric ABC complex that are important for LPS transport, some of which coordinate ATPase activity with LPS release.

PMID: 27795402 [PubMed - in process]

Progress towards generation of human haematopoietic stem cells.

Sat, 10/29/2016 - 8:58pm
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Progress towards generation of human haematopoietic stem cells.

Nat Cell Biol. 2016 Nov;18(11):1111-1117

Authors: Wahlster L, Daley GQ

Abstract
De novo generation of haematopoietic stem cells from different human pluripotent stem cell sources remains a high priority for haematology and regenerative medicine. At present, efficient derivation of functional haematopoietic stem cells with the capability for definitive in vivo engraftment and multi-lineage potential remains challenging. Here, we discuss recent progress and strategies to overcome obstacles that have thwarted past efforts. In addition, we review promising advances in the generation of mature blood lineages and the potential of induced pluripotent stem cells.

PMID: 27723718 [PubMed - in process]

TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.

Thu, 10/27/2016 - 7:05pm
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TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.

Blood. 2016 Oct 24;:

Authors: Gao X, Lee HY, da Rocha EL, Zhang C, Lu YF, Li D, Feng Y, Ezike J, Elmes RR, Barrasa MI, Cahan P, Li H, Daley GQ, Lodish HF

Abstract
Burst-forming unit erythroid progenitors (BFU-Es) are so-named based on their ability to generate in methylcellulose culture large colonies of erythroid cells that consist of "bursts" of smaller erythroid colonies derived from the later CFU-E Epo- dependent progenitors. "Early" BFU-E cells forming large BFU-E colonies presumably have higher capacities for self-renewal than do "late" BFU-E forming small colonies but the mechanism underlying this heterogeneity remains unknown. We show that the type III transforming growth factor (TGF)-β receptor (TβRIII) is a marker that distinguishes "early" and "late" BFU-Es. Transient elevation of TβRIII expression promotes TGF-β signaling during the early BFU-E to late BFU-E transition. Blocking TGF-β signaling by receptor kinase inhibitor increases early BFU-E cell self-renewal and total erythroblast production, suggesting the use of this type of drug in treating Epo unresponsive anemias.

PMID: 27777239 [PubMed - as supplied by publisher]

Discovery of a Series of 5,11-Dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-ones as Selective PI3K-δ/γ Inhibitors.

Wed, 10/26/2016 - 4:43am

Discovery of a Series of 5,11-Dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-ones as Selective PI3K-δ/γ Inhibitors.

ACS Med Chem Lett. 2016 Oct 13;7(10):908-912

Authors: Ferguson FM, Ni J, Zhang T, Tesar B, Sim T, Kim ND, Deng X, Brown JR, Zhao JJ, Gray NS

Abstract
Dual inhibition of PI3K-δ and PI3K-γ is an established therapeutic strategy for treatment of hematological malignancies. Reported molecules targeting PI3K-δ/γ selectively are chemically similar and based upon isoquinolin-1(2H)-one or quinazolin-4(3H)-one scaffolds. Here we report a chemically distinct series of potent, selective PI3K-δ/γ inhibitors based on a 5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one scaffold with comparable biochemical potency and cellular effects on PI3K signaling. We envisage these molecules will provide useful leads for development of next-generation PI3K-δ/γ targeting therapeutics.

PMID: 27774127 [PubMed - in process]

The LIN28B/let-7 axis is a novel therapeutic pathway in multiple myeloma.

Wed, 10/26/2016 - 4:43am

The LIN28B/let-7 axis is a novel therapeutic pathway in multiple myeloma.

Leukemia. 2016 Oct 24;:

Authors: Manier S, Powers JT, Sacco A, Glavey SV, Huynh D, Reagan MR, Salem KZ, Moschetta M, Shi J, Mishima Y, Roche-Lestienne C, Leleu X, Roccaro AM, Daley GQ, Ghobrial IM

Abstract
MYC is a major oncogenic driver of Multiple Myeloma (MM) and yet almost no therapeutic agents exist that target MYC in MM. Here we report that the let-7 biogenesis inhibitor LIN28B correlates with MYC expression in MM and is associated with adverse outcome. We also demonstrate that the LIN28B/let-7 axis modulates the expression of MYC, itself a let-7 target. Further, perturbation of the axis regulates the proliferation of MM cells in vivo in a xenograft tumor model. RNA sequencing and gene set enrichment analyses of CRISPR-engineered cells further suggest that the LIN28/let-7 axis regulates MYC and cell cycle pathways in MM. We provide proof-of-principle for therapeutic regulation of MYC through let-7 with an LNA-GapmeR containing a let-7b mimic in vivo, demonstrating that high levels of let-7 expression repress tumor growth by regulating MYC expression. These findings reveal a novel mechanism of therapeutic targeting of MYC through the LIN28B/let-7 axis in MM that may impact other MYC dependent cancers as well.Leukemia accepted article preview online, 24 October 2016. doi:10.1038/leu.2016.296.

PMID: 27773931 [PubMed - as supplied by publisher]

Mediator Undergoes a Compositional Change during Transcriptional Activation.

Wed, 10/26/2016 - 4:43am

Mediator Undergoes a Compositional Change during Transcriptional Activation.

Mol Cell. 2016 Oct 19;:

Authors: Petrenko N, Jin Y, Wong KH, Struhl K

Abstract
Mediator is a transcriptional co-activator recruited to enhancers by DNA-binding activators, and it also interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC). We demonstrate that a single Mediator complex associates with the enhancer and core promoter in vivo, indicating that it can physically bridge these transcriptional elements. However, the Mediator kinase module associates strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon depletion of the TFIIH kinase. Severing the kinase module from Mediator by removing the connecting subunit Med13 does not affect Mediator association at the core promoter but increases occupancy at enhancers. Thus, Mediator undergoes a compositional change in which the kinase module, recruited via Mediator to the enhancer, dissociates from Mediator to permit association with Pol II and the PIC. As such, Mediator acts as a dynamic bridge between the enhancer and core promoter.

PMID: 27773675 [PubMed - as supplied by publisher]

Differential contribution of the mitochondrial translation pathway to the survival of diffuse large B-cell lymphoma subsets.

Tue, 10/25/2016 - 3:27am

Differential contribution of the mitochondrial translation pathway to the survival of diffuse large B-cell lymphoma subsets.

Cell Death Differ. 2016 Oct 21;:

Authors: Norberg E, Lako A, Chen PH, Stanley IA, Zhou F, Ficarro SB, Chapuy B, Chen L, Rodig S, Shin D, Choi DW, Lee S, Shipp MA, Marto JA, Danial NN

Abstract
Diffuse large B-cell lymphomas (DLBCLs) are a highly heterogeneous group of tumors in which subsets share molecular features revealed by gene expression profiles and metabolic fingerprints. While B-cell receptor (BCR)-dependent DLBCLs are glycolytic, OxPhos-DLBCLs rely on mitochondrial energy transduction and nutrient utilization pathways that provide pro-survival benefits independent of BCR signaling. Integral to these metabolic distinctions is elevated mitochondrial electron transport chain (ETC) activity in OxPhos-DLBCLs compared with BCR-DLBCLs, which is linked to greater protein abundance of ETC components. To gain insights into molecular determinants of the selective increase in ETC activity and dependence on mitochondrial energy metabolism in OxPhos-DLBCLs, we examined the mitochondrial translation pathway in charge of the synthesis of mitochondrial DNA encoded ETC subunits. Quantitative mass spectrometry identified increased expression of mitochondrial translation factors in OxPhos-DLBCL as compared with the BCR subtype. Biochemical and functional assays indicate that the mitochondrial translation pathway is required for increased ETC activity and mitochondrial energy reserves in OxPhos-DLBCL. Importantly, molecular depletion of several mitochondrial translation proteins using RNA interference or pharmacological perturbation of the mitochondrial translation pathway with the FDA-approved inhibitor tigecycline (Tigecyl) is selectively toxic to OxPhos-DLBCL cell lines and primary tumors. These findings provide additional molecular insights into the metabolic characteristics of OxPhos-DLBCLs, and mark the mitochondrial translation pathway as a potential therapeutic target in these tumors.Cell Death and Differentiation advance online publication, 21 October 2016; doi:10.1038/cdd.2016.116.

PMID: 27768122 [PubMed - as supplied by publisher]

SIKs control osteocyte responses to parathyroid hormone.

Fri, 10/21/2016 - 7:56pm

SIKs control osteocyte responses to parathyroid hormone.

Nat Commun. 2016 Oct 19;7:13176

Authors: Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM

Abstract
Parathyroid hormone (PTH) activates receptors on osteocytes to orchestrate bone formation and resorption. Here we show that PTH inhibition of SOST (sclerostin), a WNT antagonist, requires HDAC4 and HDAC5, whereas PTH stimulation of RANKL, a stimulator of bone resorption, requires CRTC2. Salt inducible kinases (SIKs) control subcellular localization of HDAC4/5 and CRTC2. PTH regulates both HDAC4/5 and CRTC2 localization via phosphorylation and inhibition of SIK2. Like PTH, new small molecule SIK inhibitors cause decreased phosphorylation and increased nuclear translocation of HDAC4/5 and CRTC2. SIK inhibition mimics many of the effects of PTH in osteocytes as assessed by RNA-seq in cultured osteocytes and following in vivo administration. Once daily treatment with the small molecule SIK inhibitor YKL-05-099 increases bone formation and bone mass. Therefore, a major arm of PTH signalling in osteocytes involves SIK inhibition, and small molecule SIK inhibitors may be applied therapeutically to mimic skeletal effects of PTH.

PMID: 27759007 [PubMed - in process]

Pre-TCRs leverage Vβ CDRs and hydrophobic patch in mechanosensing thymic self-ligands.

Fri, 10/21/2016 - 7:56pm
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Pre-TCRs leverage Vβ CDRs and hydrophobic patch in mechanosensing thymic self-ligands.

J Biol Chem. 2016 Oct 5;:

Authors: Das DK, Mallis RJ, Duke-Cohan JS, Hussey RE, Tetteh PW, Hilton M, Wagner G, Lang MJ, Reinherz EL

Abstract
The pre-T cell receptor (preTCR) is a pTα-β heterodimer functioning in early αβ T-cell development. Although once thought to be ligand-autonomous, recent studies show that preTCRs participate in thymic repertoire formation through recognition of peptides bound to major histocompatibility molecules (pMHC). Using optical tweezers, we probe preTCR bonding with pMHC at the single molecule level. Like the αβTCR, the preTCR is a mechanosensor undergoing force-based structural transitions that dynamically enhance bond lifetimes, and exploiting allosteric control regulated via the Cβ FG loop region. The preTCR structural transitions exhibit greater reversibility than TCRαβ, and ordered force-bond lifetime curves. Higher piconewton (pN) force requires binding through both complementary determining region (CDR) loops and hydrophobic Vβ patch apposition. This patch functions in the pre-TCR as a surrogate Vα domain, fostering ligand promiscuity to favor development of β chains with self-reactivity but is occluded by α subunit replacement of pTα upon αβTCR formation. At the double negative 3 (DN3) thymocyte stage where the preTCR is first expressed, preTCR interaction with self-pMHC ligands imparts growth and survival advantages as revealed in thymic stromal cultures, imprinting fundamental self-reactivity in the T cell repertoire. Collectively, our data imply the existence of sequential mechanosensor αβTCR repertoire tuning via the preTCR.

PMID: 27707880 [PubMed - as supplied by publisher]

Communication growth in minimally verbal children with ASD: The importance of interaction.

Fri, 10/21/2016 - 7:00am
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Communication growth in minimally verbal children with ASD: The importance of interaction.

Autism Res. 2016 Oct;9(10):1093-1102

Authors: DiStefano C, Shih W, Kaiser A, Landa R, Kasari C

Abstract
Little is known about language development in children with Autism Spectrum Disorders (ASD) who remain minimally verbal past age 5. While there is evidence that children can develop language after age 5, we lack detailed information. Studies of this population generally focus on discrete language skills without addressing broader social-communication abilities. As communication and social deficits are both inherent to ASD, an examination of not only what language skills are acquired, but how those skills are used in interactions is relevant. Research in typical development has examined how communication interchanges (unbroken back-and-forth exchanges around a unified purpose) develop, which can be used as a framework for studying minimally verbal children. This study examined the interchange use by 55 children with ASD over the course of a 6-month play and engagement-based communication intervention. Half of the children received intervention sessions that also incorporated a speech-generating device (SGD). Interchanges were coded by: frequency, length, function, and initiator (child or adult). Results indicated that children initiated a large proportion of interchanges and this proportion increased over time. The average length and number of interchanges increased over time, with children in the SGD group showing even greater growth. Finally, children's total number of interchanges at baseline was positively associated with their spoken language gains over the course of intervention. This study supports the crucial relationship between social engagement and expressive language development, and highlights the need to include sustained communication interchanges as a target for intervention with this population. Autism Res 2016, 9: 1093-1102. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

PMID: 26824676 [PubMed - in process]

Optimal Bicelle q for Solution NMR Studies of Protein Transmembrane Partition.

Wed, 10/19/2016 - 4:56am
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Optimal Bicelle q for Solution NMR Studies of Protein Transmembrane Partition.

Chemistry. 2016 Oct 17;:

Authors: Piai A, Fu Q, Dev J, Chou JJ

Abstract
Structural characterization of transmembrane proteins in isotropic bicelles has become an increasingly popular application of solution NMR spectroscopy, as the fast-tumbling bicelles are membrane-like yet can often yield spectral quality comparable to those of detergent micelles. While larger bicelles are closer to the true lipid bilayer, it remains unclear how large the bicelles need to be to allow accurate assessment of protein transmembrane partition in lipid bilayer. Here, we address the above question from the perspective of protein residing in the bicelles, through systematic measurement of protein chemical shift and transmembrane partition at different lipid:detergent ratios (q), ranging from 0.3 to 0.7, using the transmembrane domain of human Fas receptor as model system. We found that the lipid environment of the bicelles, as reflected by the protein chemical shift, begins to be perturbed when the q is reduced to below 0.6. We also implemented a solvent paramagnetic relaxation enhancement (PRE) approach for bicelles to show that the protein transmembrane partition in bicelles with q = 0.5 and 0.7 are very similar, but at q = 0.3 the solvent PRE profile is significantly different. Our data indicate that q values between 0.5 and 0.6 are good compromise between high resolution NMR and closeness to the membrane environment, and allow accurate characterization of protein position in lipid bilayer.

PMID: 27747952 [PubMed - as supplied by publisher]

Compounds that select against the tetracycline-resistance efflux pump.

Wed, 10/19/2016 - 4:56am
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Compounds that select against the tetracycline-resistance efflux pump.

Nat Chem Biol. 2016 Sep 19;:

Authors: Stone LK, Baym M, Lieberman TD, Chait R, Clardy J, Kishony R

Abstract
We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.

PMID: 27642863 [PubMed - as supplied by publisher]

Taking Exception to Human Eugenics.

Tue, 10/18/2016 - 3:43am
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Taking Exception to Human Eugenics.

Genetics. 2016 Oct;204(2):821-823

Authors: Roth FP, Wakeley J

PMID: 27729496 [PubMed - in process]

Leucine-rich repeat kinase 2 (LRRK2) and Parkinson's disease.

Wed, 10/12/2016 - 9:24pm
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Leucine-rich repeat kinase 2 (LRRK2) and Parkinson's disease.

Proteomics. 2016 Oct 10;:

Authors: Kang UB, Marto JA

Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large multi-domain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target. Here we review the current understanding for LRRK2 function in normal physiology and PD, with emphasis on insight gained from proteomic approaches. This article is protected by copyright. All rights reserved.

PMID: 27723254 [PubMed - as supplied by publisher]