Dissociation of recombinant prion autocatalysis from infectivity

ABSTRACT

Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication – that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and non-infectious pair of autocatalytic recombinant PrP conformers derived from the same initial prion strain.¹ Noble GP, Wang DW, Walsh DJ, Barone JR, Miller MB, Nishina KA, Li S, Supattapone S. A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers. PLoS Pathog 2015; 11:e1005017; PMID:26125623; http://dx.doi.org/10.1371/journal.ppat.1005017[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] We identified restricted, C-terminal structural differences between these 2 conformers and provided evidence that these relatively subtle differences prevent the non-infectious conformer from templating the conversion of native PrP^C substrates containing a glycosylphosphatidylinositol (GPI) anchor.¹ Noble GP, Wang DW, Walsh DJ, Barone JR, Miller MB, Nishina KA, Li S, Supattapone S. A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers. PLoS Pathog 2015; 11:e1005017; PMID:26125623; http://dx.doi.org/10.1371/journal.ppat.1005017[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] In this article we discuss a model, consistent with these findings, in which recombinant PrP, lacking post-translational modifications and associated folding constraints, is capable of adopting a wide variety of autocatalytic conformations. Only a subset of these recombinant conformers can be adopted by post-translationally modified native PrP^C, and this subset represents the recombinant conformers with high specific infectivity. We examine this model's implications for the generation of highly infectious recombinant prions and the protein-only hypothesis of prion replication.     

Computer simulations of the two-species model for the melting curve maximum

The existence of extrema, maximum and/or minimum and negative gradients of melting curves observed for several elements at high pressure is investigated by molecular dynamics simulation using the two-species model (TSM) proposed by Ogura et al. [1 OguraH, MatsudaH, OgawaT, OgitaN, UedaA. Computer simulation for the melting curve maximum phenomenon. Prog Theor Phys. 1977;58:419–433.[Crossref], [Web of Science ®] , [Google Scholar]]. TSM is a model which imitates the change in the electronic structure of an atom in terms of a species change in particles. The TSM phase diagram has two solid phases and one liquid phase with a solid–solid–liquid triple point which corresponds to the melting curve minimum. The melting curve has both a maximum and a minimum, and the gradient of the melting curve is negative between these extrema. These peculiar melting curve properties and phase diagram are common to alkali metals and some other elements.     

Prion-specific Hsp40 function: The role of the auxilin homolog Swa2

Yeast prions are protein-based genetic elements that propagate through cell populations via cytosolic transfer from mother to daughter cell. Molecular chaperone proteins including Hsp70, the Hsp40/J-protein Sis1, and Hsp104 are required for continued prion propagation, however the specific requirements of chaperone proteins differ for various prions. We recently reported that Swa2, the yeast homolog of the mammalian protein auxilin, is specifically required for the propagation of the prion [URE3].¹ Troisi EM, Rockman ME, Nguyen PP, Oliver EE, Hines JK. Swa2, the yeast homolog of mammalian auxilin, is specifically required for the propagation of the prion variant [URE3-1]. Mol Microbiol 2015; 97:926-41; PMID:26031938; https://doi.org/10.1111/mmi.13076[Crossref], [PubMed], [Web of Science ®] [Google Scholar] [URE3] propagation requires both a functional J-domain and the tetratricopeptide repeat (TPR) domain of Swa2, but does not require Swa2 clathrin binding. We concluded that the TPR domain determines the specificity of the genetic interaction between Swa2 and [URE3], and that this domain likely interacts with one or more proteins with a C-terminal EEVD motif. Here we extend that analysis to incorporate additional data that supports this hypothesis. We also present new data eliminating Hsp104 as the relevant Swa2 binding partner and discuss our findings in the context of other recent work involving Hsp90. Based on these findings, we propose a new model for Swa2's involvement in [URE3] propagation in which Swa2 and Hsp90 mediate the formation of a multi-protein complex that increases the number of sites available for Hsp104 disaggregation.     

Mercury risks versus nutritional benefits of tribal commercial fish harvests in the Upper Laurentian Great Lakes

The Inter-Tribal Fisheries and Assessment Program (ITFAP) of the Chippewa Ottawa Resource Authority (CORA) in Sault Ste. Marie, Michigan, has been monitoring contaminant concentrations in the fillet portions of lake trout (Salvelinus namaycush) and lake whitefish (Coregonus clupeaformis) from the waters of lakes Superior, Huron, and Michigan since 1991. The primary purpose of this article is to present a risk quantification of methylmercury (MeHg) that is adjusted for nutritional benefit, originally presented by Ginsberg and Toal (2009 Ginsberg GL and Toal BF. 2009. Quantitative approach for incorporating methylmercury risks and omega-3 fatty acid benefits in developing species-specific fish consumption advice. Environ Health Perspect 117:267–75[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 2015) on trends in contaminant concentrations in fillet portions of these commercial fish that we recently reported in Dellinger et al. (2014 Dellinger JA, Moths MD, Dellinger M, et al. 2014. Contaminant trends in freshwater fish from the Great Lakes: A 20 year analysis. Hum Ecol Risk Assess 20:461–78[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]). Both species of fish caught by tribal fishermen showed clear benefits to cardiovascular health and infant neurodevelopment if consumed at a rate of six ounces per week. However, other popularly consumed fish such as cod, tuna, and tilapia are estimated to have only marginal benefit or net negative effects on cardiovascular health and infant neurodevelopment. This dynamic assessment of benefits and risks further demonstrates the importance of traditionally caught fish in tribal health.     

The influence of the geometry of the porcine cornea on the biomechanical response of inflation tests

To withstand the high probability of success, the growing diffusion of laser surgery for the correction of visual defects, corneal surgeons are regarding with interest numerical tools able to provide reliable predictions of the intervention outcomes. The main obstacle to the definition of a predictive numerical instrument is the objective difficulty in evaluating the in vivo mechanical properties of the human cornea. In this study, we assess the ability of a parametrised numerical model of the cornea (Pandolfi and Manganiello 2006 PandolfiA, ManganielloF. 2006. A model for the human cornea: constitutive formulation and numerical analysis. Biomech Model Mechanobiol. 5:237–246.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) to describe individual pressurisation tests on whole porcine corneas once the mechanical parameters of the model have been calibrated over average data. We also aim at estimating the sensitivity of the mechanical response with the variation of basic geometrical parameters, such as the central corneal thickness, the curvature and the in-plane diameter. We conclude that the actual geometry of a cornea has a minor role in the overall mechanical response, and therefore the material properties must be considered carefully and individually in any numerical application. This study makes use of the data obtained from a wide experimental program, where a set of 21 porcine corneas has been fully characterised in terms of mechanical and geometrical properties (Boschetti et al. 2012 BoschettiF, TriaccaV, SpinelliL, PandolfiA. 2012. Mechanical characterization of porcine corneas. J Biomech Eng. 134(3):031003.[Crossref], [Web of Science ®] , [Google Scholar]).     

VEGF-A121a binding to Neuropilins – A concept revisited

All known splice isoforms of vascular endothelial growth factor A (VEGF-A) can bind to the receptor tyrosine kinases VEGFR-1 and VEGFR-2. We focus here on VEGF-A121a and VEGF-A165a, two of the most abundant VEGF-A splice isoforms in human tissue^{1 Kut C, Mac Gabhann F, Popel AS. Where is VEGF in the body? A meta-analysis of VEGF distribution in cancer. Br J Cancer. 2007;97:978-85. doi:10.1038/sj.bjc.6603923. PMID:17912242.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]}, and their ability to bind the Neuropilin co-receptors NRP1 and NRP2. The Neuropilins are key vascular, immune, and nervous system receptors on endothelial cells, neuronal axons, and regulatory T cells respectively. They serve as co-receptors for the Plexins in Semaphorin binding on neuronal and vascular endothelial cells, and for the VEGFRs in VEGF binding on vascular and lymphatic endothelial cells, and thus regulate the initiation and coordination of cell signaling by Semaphorins and VEGFs.^{2 Guo HF, Vander Kooi CW. Neuropilin Functions as an Essential Cell Surface Receptor. J Biol Chem. 2015;290:29120-6. doi:10.1074/jbc.R115.687327. PMID:26451046.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]} There is conflicting evidence in the literature as to whether only heparin-binding VEGF-A isoforms – that is, isoforms with domains encoded by exons 6 and/or 7 plus 8a – bind to Neuropilins on endothelial cells. While it is clear that VEGF-A165a binds to both NRP1 and NRP2, published studies do not all agree on the ability of VEGF-A121a to bind NRPs. Here, we review and attempt to reconcile evidence for and against VEGF-A121a binding to Neuropilins. This evidence suggests that, in vitro, VEGF-A121a can bind to both NRP1 and NRP2 via domains encoded by exons 5 and 8a; in the case of NRP1, VEGF-A121a binds with lower affinity than VEGF-A165a. In in vitro cell culture experiments, both NRP1 and NRP2 can enhance VEGF-A121a-induced phosphorylation of VEGFR2 and downstream signaling including proliferation. However, unlike VEGFA-165a, experiments have shown that VEGF-A121a does not ‘bridge’ VEGFR2 and NRP1, i.e. it does not bind both receptors simultaneously at their extracellular domain. Thus, the mechanism by which Neuropilins potentiate VEGF-A121a-mediated VEGFR2 signaling may be different from that for VEGF-A165a. We suggest such an alternate mechanism: interactions between NRP1 and VEGFR2 transmembrane (TM) and intracellular (IC) domains.     

Interlinked bistable mechanisms generate robust mitotic transitions

The transitions between phases of the cell cycle have evolved to be robust and switch-like, which ensures temporal separation of DNA replication, sister chromatid separation, and cell division. Mathematical models describing the biochemical interaction networks of cell cycle regulators attribute these properties to underlying bistable switches, which inherently generate robust, switch-like, and irreversible transitions between states. We have recently presented new mathematical models for two control systems that regulate crucial transitions in the cell cycle: mitotic entry and exit,¹ Mochida S, Rata S, Hino H, Nagai T, Novák B. Two Bistable Switches Govern M Phase Entry. Curr Biol. 2016;26:3361-3367. doi:10.1016/j.cub.2016.10.022. PMID:27889260[Crossref], [PubMed], [Web of Science ®] [Google Scholar] and the mitotic checkpoint.² Mirkovic M, Hutter LH, Novák B, Oliveira RA. Premature sister chromatid separation is poorly detected by the spindle assembly checkpoint as a result of system-level feedback. Cell Rep. 2015;13:469-478. doi:10.1016/j.celrep.2015.09.020[Crossref], [PubMed], [Web of Science ®] [Google Scholar] Each of the two control systems is characterized by two interlinked bistable switches. In the case of mitotic checkpoint control, these switches are mutually activating, whereas in the case of the mitotic entry/exit network, the switches are mutually inhibiting. In this Perspective we describe the qualitative features of these regulatory motifs and show that having two interlinked bistable mechanisms further enhances robustness and irreversibility. We speculate that these network motifs also underlie other cell cycle transitions and cellular transitions between distinct biochemical states.     

Synthesis and Biological Evaluations of Click-Generated Nitrogen Mustards

This paper describes the synthesis of new click-generated nitrogen mustards and their biological evaluation. By using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction, we managed to synthesize eight new nitrogen mustards. This strategy paves the way for the synthesis of a new family of nitrogen mustard, with an important structural variability. Furthermore, we studied the biological activity of synthesized compounds by testing their cytotoxicity on four representative cancer cell lines A431, JURKAT, K562, and U266. One structure, 1-benzyl-4-(N,N-di-2-chloroethylaminomethyl)-1H-[1 Noll, D.M.; McG.Mason, T.; Miller, P.S. Formation and repair of interstrand cross-links in DNA. Chem. Rev. 2006, 106, 277–301.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar],2 Rink, S.M.; Hopkins, P.B. Direct evidence for DNA intrastrand cross-linking by the nitrogen mustard mechlorethamine in synthetic oligonucleotides. Bioorg. Med. Chem. Lett. 1995, 5(23), 2845–2850.[Crossref], [Web of Science ®] , [Google Scholar],3 Chabner, B.A.; Collins, J.M. Cancer Chemotherapy: Principles and Practices, PA, J.B. Lippincott Company, Philadelphia, 1990, pp. 276–313. [Google Scholar]]triazole, showed an interesting cytotoxic effect.     

Enhancer modularity and the evolution of new traits

ABSTRACT

Animals have modular cis-regulatory regions in their genomes, and expression of a single gene is often regulated by multiple enhancers residing in such a region. In the laboratory, and also in natural populations, loss of an enhancer can result in a loss of gene expression. Although only a few examples have been well characterized to date, some studies have suggested that an evolutionary gain of a new enhancer function can establish a new gene expression domain. Our recent study showed that Drosophila guttifera has more enhancers and additional expression domains of the wingless gene during the pupal stage, compared to D. melanogaster, and that these new features appear to have evolved in the ancestral lineage leading to D. guttifera.¹ Koshikawa S, Giorgianni MW, Vaccaro K, Kassner VA, Yoder JH, Werner T, Carroll SB. Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila. Proc Natl Acad Sci USA 2015; 112:7524-9; PMID:26034272; http://dx.doi.org/10.1073/pnas.1509022112[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Gain of a new expression domain of a developmental regulatory gene (toolkit gene), such as wingless, can cause co-option of the expression of its downstream genes to the new domain, resulting in duplication of a preexisting structure at this new body position. Recently, with the advancement of evo-devo studies, we have learned that the developmental regulatory systems are strikingly similar across various animal taxa, in spite of the great diversity of the animals' morphology. Even behind “new” traits, co-options of essential developmental genes from known systems are very common. We previously provided concrete evidence of gains of enhancer activities of a developmental regulatory gene underlying gains of new traits.¹ Koshikawa S, Giorgianni MW, Vaccaro K, Kassner VA, Yoder JH, Werner T, Carroll SB. Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila. Proc Natl Acad Sci USA 2015; 112:7524-9; PMID:26034272; http://dx.doi.org/10.1073/pnas.1509022112[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Broad occurrence of this scenario is testable and should be validated in the future.     

CaV2 channel subtype expression in rat sympathetic neurons is selectively regulated by α2δ subunits

Type two voltage gated calcium (Ca_V2) channels are the primary mediators of neurotransmission at neuronal presynapses, but their function at neural soma is also important in regulating excitability.¹ Catterall WA. Voltage-gated calcium channels. Cold Spring Harb Perspect Biol. 2011;3:a003947. doi:10.1101/cshperspect.a003947. PMID:21746798[Crossref], [PubMed], [Web of Science ®] [Google Scholar] Mechanisms that regulate Ca_V2 channel expression at synapses have been studied extensively, which motivated us to perform similar studies in the soma. Rat sympathetic neurons from the superior cervical ganglion (SCG) natively express Ca_V2.2 and Ca_V2.3.² Zhu Y, Ikeda SR. Adenosine modulates voltage-gated Ca2+ channels in adult rat sympathetic neurons. J Neurophysiol. 1993;70:610-20. PMID:8410161[PubMed], [Web of Science ®] [Google Scholar] We noted previously that heterologous expression of Ca_V2.1 but not Ca_V2.2 results in increased calcium current in SCG neurons.³ Beqollari D, Kammermeier PJ. The interaction between mGluR1 and the calcium channel Cav(2).(1) preserves coupling in the presence of long Homer proteins. Neuropharmacology. 2013;66:302-10. doi:10.1016/j.neuropharm.2012.05.038. PMID:22659088[Crossref], [PubMed], [Web of Science ®] [Google Scholar] In the present study, we extended these observations to show that both Ca_V2.1 and Ca_V2.3 expression resulted in increased calcium currents while Ca_V2.2 expression did not. Further, Ca_V2.1 could displace native Ca_V2.2 channels, but Ca_V2.3 expression could not. Heterologous expression of the individual accessory subunits α₂δ-1, α₂δ-2, α₂δ-3, or β4 alone failed to increase current density, suggesting that the calcium current ceiling when Ca_V2.2 was over-expressed was not due to lack of these subunits. Interestingly, introduction of recombinant α2δ subunits produced surprising effects on displacement of native Ca_V2.2 by recombinant channels. Both α₂δ-1 and α₂δ-2 seemed to promote Ca_V2.2 displacement by recombinant channel expression, while α₂δ-3 appeared to protect Ca_V2.2 from displacement. Thus, we observe a selective prioritization of Ca_V channel functional expression in neurons by specific α₂δ subunits. These data highlight a new function for α₂δ subtypes that could shed light on subtype selectivity of Ca_V2 membrane expression.     

Teaching Bernoulli's Principle through Demonstrations

ABSTRACT

One proven strategy to help students make sense of abstract concepts is to sequence instruction so students have exploratory opportunities to investigate science before being introduced to new science explanations (Abraham and Renner 1986 Abraham, M. R. and Renner, J. W. 1986. The sequence of learning cycle activities in high school chemistry. Journal of Research in Science Teaching, 23: 121–143. [Crossref], [Web of Science ®] , [Google Scholar]; Renner, Abraham, and Birnie 1988 Renner, J. W., Abraham, M. R. and Birnie, H. H. 1988. The necessity of each phase of the learning cycle in teaching high school physics. Journal of Research in Science Teaching, 25: 39–58. [Crossref], [Web of Science ®] , [Google Scholar]). To help physical science teachers make sense of how to effectively sequence lessons, this article summarizes our experiences using an exploration–explanation sequence of instruction to teach Bernoulli's principle to prospective middle and secondary science teachers in a science methods course. We use demonstrations during our Bernoulli unit to help students go back and forth between their observations of phenomenon and what occurs on the microscopic level with what we have termed molecular talk. Students engage in guiding questions, consider their old and new understandings of science, and use evidence to construct new ideas during all stages of the lesson.     

The tumor suppressor Lgl1 regulates front-rear polarity of migrating cells

Cell migration is a highly integrated, multistep process that plays an important role in physiological and pathological processes. The migrating cell is highly polarized, with complex regulatory pathways that integrate its component processes spatially and temporally.¹ Ridley AJ, Schwartz MA, Burridge K, Firtel RA, Ginsberg MH, Borisy G, Parsons JT, Horwitz AR. Cell migration: integrating signals from front to back. Science 2003; 302:1704-9; PMID:14657486; http://dx.doi.org/10.1126/science.1092053[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] The Drosophila tumor suppressor, Lethal (2) giant larvae (Lgl), regulates apical-basal polarity in epithelia and asymmetric cell division.² Etienne-Manneville S. Polarity proteins in migration and invasion. Oncogene 2008; 27:6970-80; PMID:19029938; http://dx.doi.org/10.1038/onc.2008.347[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] But little is known about the role of Lgl in establishing cell polarity in migrating cells. Recently, we showed that the mammalian Lgl1 interacts directly with non-muscle myosin IIA (NMIIA), inhibiting its ability to assemble into filaments in vitro.³ Dahan I, Yearim A, Touboul Y, Ravid S. The tumor suppressor Lgl1 regulates NMII-A cellular distribution and focal adhesion morphology to optimize cell migration. Mol Biol Cell 2012; 23:591-601; PMID:22219375; http://dx.doi.org/10.1091/mbc.E11-01-0015[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Lgl1 also regulates the cellular localization of NMIIA, the maturation of focal adhesions, and cell migration.³ Dahan I, Yearim A, Touboul Y, Ravid S. The tumor suppressor Lgl1 regulates NMII-A cellular distribution and focal adhesion morphology to optimize cell migration. Mol Biol Cell 2012; 23:591-601; PMID:22219375; http://dx.doi.org/10.1091/mbc.E11-01-0015[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] We further showed that phosphorylation of Lgl1 by aPKCζ prevents its interaction with NMIIA and is important for Lgl1 and acto-NMII cytoskeleton cellular organization.⁴ Dahan I, Petrov D, Cohen-Kfir E, Ravid S. The tumor suppressor Lgl1 forms discrete complexes with NMII-A and Par6α-aPKCζ that are affected by Lgl1 phosphorylation. J Cell Sci 2014; 127:295-304; PMID:24213535; http://dx.doi.org/10.1242/jcs.127357[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Lgl is a critical downstream target of the Par6-aPKC cell polarity complex; we showed that Lgl1 forms two distinct complexes in vivo, Lgl1-NMIIA and Lgl1-Par6-aPKCζ in different cellular compartments.⁴ Dahan I, Petrov D, Cohen-Kfir E, Ravid S. The tumor suppressor Lgl1 forms discrete complexes with NMII-A and Par6α-aPKCζ that are affected by Lgl1 phosphorylation. J Cell Sci 2014; 127:295-304; PMID:24213535; http://dx.doi.org/10.1242/jcs.127357[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] We further showed that aPKCζ and NMIIA compete to bind directly to Lgl1 through the same domain. These data provide new insights into the role of Lgl1, NMIIA, and Par6-aPKCζ in establishing front-rear polarity in migrating cells. In this commentary, I discuss the role of Lgl1 in the regulation of the acto-NMII cytoskeleton and its regulation by the Par6-aPKCζ polarity complex, and how Lgl1 activity may contribute to the establishment of front-rear polarity in migrating cells.     

Death by over-eating: The Gaucher disease associated gene GBA1, identified in a screen for mediators of autophagic cell death,is necessary for developmental cell death in Drosophila midgut

Autophagy is critical for homeostasis and cell survival during stress, but can also lead to cell death, a little understood process that has been shown to contribute to developmental cell death in lower model organisms, and to human cancer cell death. We recently reported¹ Dasari SK, Bialik S, Levin-Zaidman S, Levin-Salomon V, Merrill AH, Jr., Futerman AH, Kimchi A. Signalome-wide rnai screen identifies gba1 as a positive mediator of autophagic cell death. Cell Death Differ. 2017;24(7):1288-1302. https://doi.org/10.1038/cdd.2017.80. PMID:28574511[Crossref], [PubMed], [Web of Science ®] [Google Scholar] on our thorough molecular and morphologic characterization of an autophagic cell death system involving resveratrol treatment of lung carcinoma cells. To gain mechanistic insight into this death program, we performed a signalome-wide RNAi screen for genes whose functions are necessary for resveratrol-induced death. The screen identified GBA1, the gene encoding the lysosomal enzyme glucocerebrosidase, as an important mediator of autophagic cell death. Here we further show the physiological relevance of GBA1 to developmental cell death in midgut regression during Drosophila metamorphosis. We observed a delay in midgut cell death in two independent Gba1a RNAi lines, indicating the critical importance of Gba1a for midgut development. Interestingly, loss-of-function GBA1 mutations lead to Gaucher Disease and are a significant risk factor for Parkinson Disease, which have been associated with defective autophagy. Thus GBA1 is a conserved element critical for maintaining proper levels of autophagy, with high levels leading to autophagic cell death.     

Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds

In total 52 samples of Sahiwal (19 Excoffier L, Laval G, Schneider S. Arlequin 3.01: An integrated software package for population genetics data analysis. Evol Bioinform Online 2005; 1:47–50.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), Tharparkar (17 Hayes BJ, Bowman PJ, Chamberlain, AJ, Goddard ME. Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 2009; 92:433–443.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), and Gir (16 Melka HD, Jeon EK, Kim SW, Han JB, Yoon D, Kim KS. Identification of genomic differences between Hanwoo and Holstein breeds using the Illumina Bovine SNP50 BeadChip. Genomics Inform 2011; 9:69–73.[Crossref] , [Google Scholar]) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%?50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248?±?0.006, 0.241?±?0.007, and 0.242?±?0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold’s genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r²?相似文献   

Tyr(less) kinase signaling during mitosis

Tyrosine phosphorylation is rare, representing only about 0.5% of phosphorylations in the cell under basal conditions. While mitogenic tyrosine kinase signaling has been extensively explored, the role of phosphotyrosine signaling across the cell cycle and in particular during mitosis is poorly understood.

Two recent, independent studies tackled this question from different angles to reveal exciting new insights into the role of this modification during cell division. Caron et al.¹ Caron D, Byrne DP, Thebault P, Soulet D, Landry CR, Eyers PA, Elowe S. Mitotic phosphotyrosine network analysis reveals that tyrosine phosphorylation regulates Polo-like kinase 1 (PLK1). Sci Signal 2016; 9:rs14; PMID:27965426; http://dx.doi.org/10.1126/scisignal.aah3525[Crossref], [PubMed], [Web of Science ®] [Google Scholar] exploited mitotic phosphoproteomics data sets to determine the extent of mitotic tyrosine phosphorylation, and St-Denis et al.² St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, et al. Phenotypic and interaction profiling of the human phosphatases identifies diverse mitotic regulators. Cell Rep 2016; 17:2488-501; PMID:27880917; http://dx.doi.org/10.1016/j.celrep.2016.10.078[Crossref], [PubMed], [Web of Science ®] [Google Scholar] identified protein tyrosine phosphatases from all subfamilies as regulators of mitotic progression or spindle formation. These studied collectively revealed that tyrosine phosphorylation may play a more prominent and active role in mitotic progression than previously appreciated.     

Combined tRNA modification defects impair protein homeostasis and synthesis of the yeast prion protein Rnq1

Modified nucleosides in tRNA anticodon loops such as 5-methoxy-carbonyl-methyl-2-thiouridine (mcm⁵s²U) and pseuduridine (Ψ) are thought to be required for an efficient decoding process. In Saccharomyces cerevisiae, the simultaneous presence of mcm⁵s²U and Ψ38 in tRNA^Gln_UUG was shown to mediate efficient synthesis of the Q/N rich [PIN⁺] prion forming protein Rnq1.¹ Klassen R, Ciftci A, Johanna Funk J, Bruch A, Butter F, Schaffrath R. tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast. Nucleic Acids Res 2016; 44(22):10946-959. pii: gkw705; PMID:27496282; http://dx.doi.org/10.1093/nar/gkw705[Crossref], [PubMed], [Web of Science ®] [Google Scholar] In the absence of these two tRNA modifications, higher than normal levels of hypomodified tRNA^Gln_UUG, but not its isoacceptor tRNA^Gln_CUG can restore Rnq1 synthesis. Moroever, tRNA overexpression rescues pleiotropic phenotypes that associate with loss of mcm⁵s²U and Ψ38 formation. Notably, combined absence of different tRNA modifications are shown to induce the formation of protein aggregates which likely mediate severe cytological abnormalities, including cytokinesis and nuclear segregation defects. In support of this, overexpression of the aggregating polyQ protein Htt103Q, but not its non-aggregating variant Htt25Q phenocopies these cytological abnormalities, most pronouncedly in deg1 single mutants lacking Ψ38 alone. It is concluded that slow decoding of particular codons induces defects in protein homeostasis that interfere with key steps in cytokinesis and nuclear segregation.