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Neandertal signatures in modern human mitochondrial genome haplogroups? [article]

Renata C Ferreira, Camila R Rodrigues, James R Broach, Marcelo RS Briones
2017 bioRxiv   pre-print
Siberia R 87.89 (35) Fumane 2 KP718913 41-39,000 Italy R 94.43 (35) Tianyuan KC417443 40,000 China B4'5 91.17 (35, 36) Kostenki 14 FN600416 39-36,000 Russia U2 92.69 (35) Doni Vestonice  ...  R. E. Green et al., A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 134, 416-426 (2008). 40. M.-T. Gansauge, M.  ... 
doi:10.1101/190363 fatcat:fj7okw6xsfe53kgmufp2p4274m

Inhibition of the Platelet-activating factor receptor for the treatment of Amyotrophic Lateral Sclerosis? [article]

Marcelo RS Briones, Amanda M Snyder, Elizabeth B Neely, James R Connor, James R Broach
2017 bioRxiv   pre-print
Cerebrospinal Fluids (CSF) of Amyotrophic Lateral Sclerosis (ALS) patients have increased levels of the inflammatory cytokine IL-18. Because IL-18 is produced by dendritic cells stimulated by the Platelet-activating factor (PAF), a major neuroinflammatory mediator, it is expected that PAF is involved in ALS. Pilot experimental data on amplification of PAF receptor (PAFR) mRNA by RT-PCR show that PAFR is overexpressed, as compared to age matched controls, in the spinal cords of transgenic ALS
more » ... se model SOD1-G93A, suggesting PAF mediation. Although anti- inflammatory drugs have been tested for ALS before, no clinical trial has been conducted using PAFR specific inhibitors. Therefore, we hypothesize that administration of PAFR inhibitors, such as Ginkgolide B, PCA 4248 and WEB 2086, have potential to function as a novel therapy for ALS, particularly in SOD1 familial ALS forms. Because currently there are only two approved drugs with modest effectiveness for ALS therapy, a search for novel drugs and targets is essential.
doi:10.1101/224030 fatcat:i6a7eh2ac5cytnvlydmcjpfp5q

A Possible Role for Platelet-Activating Factor Receptor in Amyotrophic Lateral Sclerosis Treatment

Marcelo R. S. Briones, Amanda M. Snyder, Renata C. Ferreira, Elizabeth B. Neely, James R. Connor, James R. Broach
2018 Frontiers in Neurology  
The first efficacy and safety trial do not to demonstrate edaravone efficacy in a confirmatory study with primary outcome based on the ALS functional rating scale (ALSFRS-R) scores (27) .  ...  onset within two years and greater-efficacy-expected subpopulation within the efficacyexpected population with% forced vital capacity of ≥80%, and ≥2 points for all item scores in the revised ALSFRS-R  ... 
doi:10.3389/fneur.2018.00039 pmid:29472887 pmcid:PMC5810282 fatcat:hgewbf2i2baihawcyvreubpbse

Chromosomal boundaries in S. cerevisiae

Xin Bi, James R Broach
2001 Current Opinion in Genetics and Development  
Since wrapping of DNA on a nucleosomal core particle Chromosomal boundaries in S. cerevisiae Xin Bi* and James R Broach † introduces an average ∆Lk of ~-1, losing two nucleosomes would cause local DNA  ...  B, Abf1; R, Rap1; O, ORC; Sirs, complex of Sir2, Sir3 and Sir4. Figure 3 3 Domain organization by directional initiation of heterochromatin.  ... 
doi:10.1016/s0959-437x(00)00179-9 pmid:11250144 fatcat:mqvijvhh2bb5dj3gbodgmjuahu

Single-Cell Observations Reveal Intermediate Transcriptional Silencing States

Eugenia Y. Xu, Karl A. Zawadzki, James R. Broach
2006 Molecular Cell  
Table 2 . 2 Rates of Interconversion between Active and Repressed Mating Type Loci in sir1 Cells Locus PPR1 Repressed (R) Derepressed (DR) R / DR (k 1 , gen 21 ) D R/ R (k 21 , gen 21 ) K D (DR/R  ...  the ratio of DR to R cells, which should be equal to the rate of conversion from DR to R cells divided by the rate of conversion from R to DR cells.  ... 
doi:10.1016/j.molcel.2006.05.035 pmid:16857588 fatcat:xiopcgjjnjf6vkynubsq3fcsle

The Dynamics of Homologous Pairing during Mating Type Interconversion in Budding Yeast

Peter L. Houston, James R. Broach
2006 PLoS Genetics  
Citation: Houston PL, Broach JR (2006) The dynamics of homologous pairing during mating type interconversion in budding yeast. PLoS Genet 2(6): e98.  ... 
doi:10.1371/journal.pgen.0020098 pmid:16789829 pmcid:PMC1480535 fatcat:7w3sjw7xv5bkdnzdzm5sfztv5u

Genetic properties of chromosomally integrated 2μ plasmid DNA in yeast

S.Carl Falco, Yuyang Li, James R. Broach, David Botstein
1982 Cell  
and Hicks, 1980; Broach, 1981) .  ...  Efficient interconversion requires an intact FLP gene and appears to be a form of site-specific recombination (Broach and Hicks, 1980; Broach et al., 1982) .  ... 
doi:10.1016/0092-8674(82)90173-8 pmid:6288264 fatcat:cvgxzylpmngfdmpyleomla6aba

Creation of GPCR-based chemical sensors by directed evolution in yeast

Addison D. Ault, James R. Broach
2005 Protein Engineering Design & Selection  
Acknowledgements The authors thank Amber Hobart for assistance cloning the UDPG expression vector and members of the Broach laboratory for helpful discussions.  ...  T R CAT GCG ACC CGG H-17 H A T R CAT GCC ACT AGA H-6 H V L R CAC GCG TTG CGT H-7 H I C R CAT ATT TGC CGG H-8 H T L R CAC ACG CTG CGA H-10 H V I R CAC GTT ATC CGA H-11  ...  II Sequences of recovered HIAR mutants a Clone AA position DNA sequence H I A R H-1 H A V R CAC GCG GTG AAG H-2 H A L R CAC GCA TTG CGG H-5 H A T R CAC GCG ACA AGA H-9 H A  ... 
doi:10.1093/protein/gzi069 pmid:16263727 fatcat:ptjis2crcncvvin6r2cf7hpltm

Acousto-electromagnetic sensor for locating land mines

Waymond R. Scott, Jr., Christoph T. Schroeder, James S. Martin, Abinash C. Dubey, James F. Harvey, J. Thomas Broach
1998 Detection and Remediation Technologies for Mines and Minelike Targets III  
At time #1, pressure (P), shear (S), and surface (R) waves are seen to be launched.  ... 
doi:10.1117/12.324189 fatcat:kbb4s6ddpfcrzdtsvskojc646e

The yeast genome undergoes significant topological reorganization in quiescence

Mark T. Rutledge, Mariano Russo, Jon-Matthew Belton, Job Dekker, James R. Broach
2015 Nucleic Acids Research  
All data analysis of the normalized data was performed in R.  ...  The results were visualized in R using a custom script making use of the following libraries: ggplot2, RColorBrewer, plyr, reshape2.  ... 
doi:10.1093/nar/gkv723 pmid:26202961 pmcid:PMC4787801 fatcat:rgpt24puavdfnbn2uhmj5onqtq

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

Erika Shor, Catherine A. Fox, James R. Broach, Sue Jinks-Robertson
2013 PLoS Genetics  
This figure shows FOA R rates from Figure 5B overlaid with black bars reflecting the proportion of the FOA R colonies due to ura3 mutations.  ...  Measuring FOA R mutation rate in the presence or absence of stress The FOA R mutation assay was performed similarly to that for CAN1 with a few differences.  ... 
doi:10.1371/journal.pgen.1003680 pmid:23935537 pmcid:PMC3731204 fatcat:ljzifam6sfgqzmqohpb7ulcghm

Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast

Yu Jiang, James R. Broach
1999 EMBO Journal  
Tor proteins, homologous to DNA-dependent protein kinases, participate in a signal transduction pathway in yeast that regulates protein synthesis and cell wall expansion in response to nutrient availability. The anti-inflammatory drug rapamycin inhibits yeast cell growth by inhibiting Tor protein signaling. This leads to diminished association of a protein, Tap42, with two different protein phosphatase catalytic subunits; one encoded redundantly by PPH21 and PPH22, and one encoded by SIT4. We
more » ... ow that inactivation of either Cdc55 or Tpd3, which regulate Pph21/22 activity, results in rapamycin resistance and that this resistance correlates with an increased association of Tap42 with Pph21/22. Furthermore, we show Tor-dependent phosphorylation of Tap42 both in vivo and in vitro and that this phosphorylation is rapamycin sensitive. Inactivation of Cdc55 or Tpd3 enhances in vivo phosphorylation of Tap42. We conclude that Tor phosphorylates Tap42 and that phosphorylated Tap42 effectively competes with Cdc55/Tpd3 for binding to the phosphatase 2A catalytic subunit. Furthermore, Cdc55 and Tpd3 promote dephosphorylation of Tap42. Thus, Tor stimulates growth-promoting association of Tap42 with Pph21/22 and Sit4, while Cdc55 and Tpd3 inhibit this association both by direct competition and by dephosphorylation of Tap42. These results establish Tap42 as a target of Tor and add further refinement to the Tor signaling pathway.
doi:10.1093/emboj/18.10.2782 pmid:10329624 pmcid:PMC1171359 fatcat:hrgcpunbmzbcjkt3yawk2seb2m

Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman, Soyeon I Lippman, Lisa Schneper, Noam Slonim, James R Broach
2009 Molecular Systems Biology  
doi:10.1038/msb.2009.2 pmid:19225458 pmcid:PMC2657534 fatcat:p5r2bdjcyva5lbtfqtfcrwelye

Large vibrometer arrays for seismic landmine detection

Waymond R. Scott, Jr., James O. Hamblen, James S. Martin, Gregg D. Larson, J. Thomas Broach, Russell S. Harmon, John H. Holloway, Jr.
2006 Detection and Remediation Technologies for Mines and Minelike Targets XI  
Inexpensive ground-contacting accelerometers have been demonstrated in field experiments as appropriate vibrometers for a seismic landmine detection system. A thirty-two-element line array of these has been used to detect a variety of anti-tank (AT) landmines under realistic field conditions. Images of data measured by scanning this line array to synthesize a larger plane array have shown that the two-dimensional array offers potential advantages in terms of both measurement speed and landmine
more » ... mage contrast. The simultaneity of measurements with a physical array, as compared to synthetic array measurements that have been performed in the past, presents opportunities for improved landmine detection algorithms. Issues pertaining to the implementation of large arrays of vibrometers include sensor fidelity, array fidelity, scalability, and safety. Experimental measurements with prototype sensors in the laboratory and at a field test site have demonstrated the robust and repeatable ground coupling of the sensor in sand, dirt, gravel, and grass. Ground loading has been investigated with multiple array configurations with the dominant effect being an increase in the wave speeds of the surface waves. While the field experiments with the line array were conducted using commercially available data acquisition hardware and software, a custom data acquisition and processing system has been developed to meet the requirements of a large array of sensors. A lightweight sensor ensures the safety of touching the ground over buried landmines as the contact force is significantly less than the force required to detonate typical antipersonnel (AP) landmines and AT landmines.
doi:10.1117/12.669555 fatcat:tgoovfbbjzeozb32pruy77ii6m

Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman, Soyeon I Lippman, Lisa Schneper, Noam Slonim, James R Broach
2009 Molecular Systems Biology  
doi:10.1038/msb.2009.20 fatcat:xkmow3i72nf4jk6yysagntjfhq
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