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https://www.readbyqxmd.com/read/29331951/sita-standard-perimetry-has-better-performance-than-fdt2-matrix-perimetry-for-detecting-glaucomatous-progression
#1
Michael Wall, Chris A Johnson, K D Zamba
PURPOSE: The Humphrey Matrix (FDT2) may be more sensitive in detecting glaucomatous visual field loss than SITA standard automated perimetry (SAP) performed on the Humphrey Field Analyzer (HFA). Therefore, FDT may be a good candidate to determine disease progression in patients with glaucoma. Our aim was to test the hypothesis that automated perimetry using the FDT2 would be equal to, or more effective than, HFA SITA-Standard, in identifying glaucomatous progression. METHODS: One hundred and twenty patients with glaucoma were tested twice at baseline and every 6 months for 4 years with HFA SITA-Standard and FDT2...
January 13, 2018: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/29331608/allosteric-effects-in-bacteriophage-hk97-procapsids-revealed-directly-from-covariance-analysis-of-cryo-em-data
#2
Nan Xu, David Veesler, Peter C Doerschuk, John E Johnson
The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways...
January 10, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29331591/brochosomins-and-other-novel-proteins-from-brochosomes-of-leafhoppers-insecta-hemiptera-cicadellidae
#3
Roman Rakitov, Alexander A Moysa, Arthur T Kopylov, Sergei A Moshkovskii, Ralph S Peters, Karen Meusemann, Bernhard Misof, Christopher H Dietrich, Kevin P Johnson, Lars Podsiadlowski, Kimberly K O Walden
Brochosomes (BS) are secretory granules resembling buckyballs, produced intracellularly in specialized glandular segments of the Malpighian tubules and forming superhydrophobic coatings on the integuments of leafhoppers (Hemiptera, Cicadellidae). Their composition is poorly known. Using a combination of SDS-PAGE, LC-MS/MS, next-generation sequencing (RNAseq) and bioinformatics we demonstrate that the major structural component of BS of the leafhopper Graphocephala fennahi Young is a novel family of 21-40-kDa secretory proteins, referred to herein as brochosomins (BSM), apparently cross-linked by disulfide bonds...
January 10, 2018: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29331515/mhc-class-i-loaded-ligands-from-breast-cancer-cell-lines-a-potential-hla-i-typed-antigen-collection
#4
Dmitri V Rozanov, Nikita D Rozanov, Kami Chiotti, Ashok Reddy, Phillip A Wilmarth, Larry L David, Seung W Cha, Sunghee Woo, Pavel Pevzner, Vineet Bafna, Gregory G Burrows, Juha K Rantala, Trevor Levin, Pavana Anur, Katie Johnson-Camacho, Shaadi Tabatabaei, Daniel J Munson, Tullia C Bruno, Jill E Slansky, John W Kappler, Naoto Hirano, Sebastian Boegel, Bernard A Fox, Colt Egelston, Diana L Simons, Grecia Jimenez, Peter P Lee, Joe W Gray, Paul T Spellman
To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic...
January 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29331395/tyrosine-hydroxylase-as-a-sentinel-for-central-and-peripheral-tissue-responses-in-parkinson-s-progression-evidence-from-clinical-studies-and-neurotoxin-models
#5
REVIEW
M E Johnson, M F Salvatore, S A Maiolo, L Bobrovskaya
Parkinson's disease (PD) is a common neurodegenerative disease worldwide. While the typical motor symptoms of PD are well known, the lesser known non-motor symptoms can also greatly impact the patient's quality of life. These symptoms often appear before motor impairment, therefore identifying biomarkers that may predict PD risk or pathology has been a major and challenging endeavour. Given that the loss of dopamine, and its rate-limiting enzyme tyrosine hydroxylase (TH) occurs in PD, the expression and accompanying post-translational changes in TH during PD progression could yield insight into the disruption of cellular signalling occurring in the CNS, and also in peripheral tissues wherein catecholamine function plays a role...
January 10, 2018: Progress in Neurobiology
https://www.readbyqxmd.com/read/29331124/characterizing-protein-conformations-by-correlation-analysis-of-coarse-grained-contact-matrices
#6
Richard J Lindsay, Jan Siess, David P Lohry, Trevor S McGee, Jordan S Ritchie, Quentin R Johnson, Tongye Shen
We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences...
January 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29330877/characterization-of-biologic-response-modifiers-in-the-supernatant-of-conventional-refrigerated-and-cryopreserved-platelets
#7
Lacey Johnson, Shereen Tan, Emily Jenkins, Ben Wood, Denese C Marks
BACKGROUND: Alternatives to room temperature storage of platelets (PLTs) are of interest to support blood banking logistics. The aim of this study was to compare the presence of biologic response modifiers (BRMs) in PLT concentrates stored under conventional room temperature conditions with refrigerated or cryopreserved PLTs. STUDY DESIGN AND METHODS: A three-arm pool-and-split study was carried out using buffy coat-derived PLTs stored in 30% plasma/70% SSP+. The three matched treatment arms were as follows: room temperature (20-24°C), cold (2-6°C), and cryopreserved (-80°C with DMSO)...
January 12, 2018: Transfusion
https://www.readbyqxmd.com/read/29330649/growth-of-leptospirillum-ferriphilum-in-sulfur-medium-in-co-culture-with-acidithiobacillus-caldus
#8
Sarah L Smith, D Barrie Johnson
Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, and also hydrogen, as electron donors. It has recently been demonstrated that A. caldus reduces ferric iron to ferrous when grown aerobically on sulfur. Experiments were carried out which demonstrated that this allowed L...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330524/nf-%C3%AE%C2%BAb-inducing-kinase-is-a-therapeutic-target-for-systemic-lupus-erythematosus
#9
Hans D Brightbill, Eric Suto, Nicole Blaquiere, Nandhini Ramamoorthi, Swathi Sujatha-Bhaskar, Emily B Gogol, Georgette M Castanedo, Benjamin T Jackson, Youngsu C Kwon, Susan Haller, Justin Lesch, Karin Bents, Christine Everett, Pawan Bir Kohli, Sandra Linge, Laura Christian, Kathy Barrett, Allan Jaochico, Leonid M Berezhkovskiy, Peter W Fan, Zora Modrusan, Kelli Veliz, Michael J Townsend, Jason DeVoss, Adam R Johnson, Robert Godemann, Wyne P Lee, Cary D Austin, Brent S McKenzie, Jason A Hackney, James J Crawford, Steven T Staben, Moulay H Alaoui Ismaili, Lawren C Wu, Nico Ghilardi
NF-κB-inducing kinase (NIK) mediates non-canonical NF-κB signaling downstream of multiple TNF family members, including BAFF, TWEAK, CD40, and OX40, which are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Here, we show that experimental lupus in NZB/W F1 mice can be treated with a highly selective and potent NIK small molecule inhibitor. Both in vitro as well as in vivo, NIK inhibition recapitulates the pharmacological effects of BAFF blockade, which is clinically efficacious in SLE...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#10
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330415/unusual-multiscale-mechanics-of-biomimetic-nanoparticle-hydrogels
#11
Yunlong Zhou, Pablo F Damasceno, Bagganahalli S Somashekar, Michael Engel, Falin Tian, Jian Zhu, Rui Huang, Kyle Johnson, Carl McIntyre, Kai Sun, Ming Yang, Peter F Green, Ayyalusamy Ramamoorthy, Sharon C Glotzer, Nicholas A Kotov
Viscoelastic properties are central for gels and other materials. Simultaneously, high storage and loss moduli are difficult to attain due to their contrarian requirements to chemical structure. Biomimetic inorganic nanoparticles offer a promising toolbox for multiscale engineering of gel mechanics, but a conceptual framework for their molecular, nanoscale, mesoscale, and microscale engineering as viscoelastic materials is absent. Here we show nanoparticle gels with simultaneously high storage and loss moduli from CdTe nanoparticles...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29330372/non-estrogenic-xanthohumol-derivatives-mitigate-insulin-resistance-and-cognitive-impairment-in-high-fat-diet-induced-obese-mice
#12
Cristobal L Miranda, Lance A Johnson, Oriane de Montgolfier, Valerie D Elias, Lea S Ullrich, Joshua J Hay, Ines L Paraiso, Jaewoo Choi, Ralph L Reed, Johana S Revel, Chrissa Kioussi, Gerd Bobe, Urszula T Iwaniec, Russell T Turner, Benita S Katzenellenbogen, John A Katzenellenbogen, Paul R Blakemore, Adrian F Gombart, Claudia S Maier, Jacob Raber, Jan F Stevens
Xanthohumol (XN), a prenylated flavonoid from hops, improves dysfunctional glucose and lipid metabolism in animal models of metabolic syndrome (MetS). However, its metabolic transformation into the estrogenic metabolite, 8-prenylnaringenin (8-PN), poses a potential health concern for its use in humans. To address this concern, we evaluated two hydrogenated derivatives, α,β-dihydro-XN (DXN) and tetrahydro-XN (TXN), which showed negligible affinity for estrogen receptors α and β, and which cannot be metabolically converted into 8-PN...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330241/primary-care-physician-involvement-in-shared-decision-making-for-critically-ill-patients-and-family-satisfaction-with-care
#13
Kevin B Huang, Urs Weber, Jennifer Johnson, Nathanial Anderson, Andrea K Knies, Belinda Nhundu, Cynthia Bautista, Kelly Poskus, Kevin N Sheth, David Y Hwang
PURPOSE: An intensive care unit (ICU) patient's primary care physician (PCP) may be able to assist family with certain ICU shared medical decisions. We explored whether families of patients in nonopen ICUs who nevertheless report involvement of a patient's PCP in medical decision making are more satisfied with ICU shared decision making than families who do not. METHODS: Between March 2013 and December 2015, we administered the Family Satisfaction in the ICU 24 survey to family members of adult neuroscience ICU patients...
January 2018: Journal of the American Board of Family Medicine: JABFM
https://www.readbyqxmd.com/read/29330218/a-study-on-pharmacokinetics-of-bosentan-with-systems-modeling-part-1-translating-systemic-plasma-concentration-to-liver-exposure-in-healthy-subjects
#14
Rui Li, Mark Niosi, Nathaniel Johnson, David A Tess, Emi Kimoto, Jian Lin, Xin Yang, Keith A Riccardi, Sangwoo Ryu, Ayman F El-Kattan, Tristan S Maurer, Larry M Tremaine, Li Di
Understanding liver exposure of hepatic transporter substrates in clinical studies is often critical as it typically governs pharmacodynamics, drug-drug interactions, and toxicity for certain drugs. However, this is a challenging task since there is currently no easy method to directly measure drug concentration in the human liver. Using bosentan as an example, a new approach has been demonstrated to estimate liver exposure based on observed systemic pharmacokinetics from clinical studies using physiologically-based pharmacokinetic modeling...
January 12, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29330018/testicular-adrenal-rest-tumor-screening-and-fertility-counseling-among-males-with-congenital-adrenal-hyperplasia
#15
Monika Chaudhari, Emilie K Johnson, Daniel DaJusta, Leena Nahata
BACKGROUND: Reduced fertility is a common potential problem among males with congenital adrenal hyperplasia (CAH), with nearly half experiencing impaired sperm production. The major cause of oligo/azoospermia in CAH is testicular adrenal rest tumors (TARTs). Studies indicate that ultrasound screening for TARTs should begin during childhood, yet it remains unclear whether boys with CAH are routinely screened for TARTs and/or counseled about infertility risk and potential interventions such as fertility testing and/or preservation...
December 21, 2017: Journal of Pediatric Urology
https://www.readbyqxmd.com/read/29329757/challenges-of-francisella-classification-exemplified-by-an-atypical-clinical-isolate
#16
L M Matz, K Y Kamdar, M E Holder, G A Metcalf, G M Weissenberger, Q Meng, V Vee, Y Han, D M Muzny, R A Gibbs, C L Johnson, P A Revell, J F Petrosino
The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F...
December 6, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29329284/identification-of-an-elaborate-nk-specific-system-regulating-hla-c-expression
#17
Hongchuan Li, Martin A Ivarsson, Victoria E Walker-Sperling, Jeff Subleski, Jenna K Johnson, Paul W Wright, Mary Carrington, Niklas K Björkström, Daniel W McVicar, Stephen K Anderson
The HLA-C gene appears to have evolved in higher primates to serve as a dominant source of ligands for the KIR2D family of inhibitory MHC class I receptors. The expression of NK cell-intrinsic MHC class I has been shown to regulate the murine Ly49 family of MHC class I receptors due to the interaction of these receptors with NK cell MHC in cis. However, cis interactions have not been demonstrated for the human KIR and HLA proteins. We report the discovery of an elaborate NK cell-specific system regulating HLA-C expression, indicating an important role for HLA-C in the development and function of NK cells...
January 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29329106/genetic-mutations-associated-with-neonatal-diabetes-mellitus-in-omani-patients
#18
Aisha Al Senani, Nishath Hamza, Hanan Al Azkawi, Manal Al Kharusi, Nashat Al Sukaiti, Maryam Al Badi, Moza Al Yahyai, Matthew Johnson, Elisa De Franco, Sarah Flanagan, Andrew Hattersley, Sian Ellard, Waad-Allah Mula-Abed
BACKGROUND: Neonatal diabetes mellitus (NDM) is a rare disorder worldwide where diabetes is diagnosed in the first 6 months of life. However, Oman has a relatively high incidence of NDM. METHODS: In this study, we investigated the genetic etiologies underlying NDM and their prevalence in Oman. We collected a cohort of 24 NDM patients, with and without genetic diagnosis, referred to our center from 2007 to 2015. All patients without a genetic diagnosis were tested for mutations in 23 NDM-associated genes using a custom-targeted next-generation sequencing (NGS) panel and methylation analysis of the 6q24 locus...
January 12, 2018: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/29328957/sphingolipids-in-host-microbial-interactions
#19
REVIEW
Stacey L Heaver, Elizabeth L Johnson, Ruth E Ley
Sphingolipids, a lipid class characterized by a long-chain amino alcohol backbone, serve vital structural and signaling roles in eukaryotes. Though eukaryotes produce sphingolipids, this capacity is phylogenetically highly restricted in Bacteria. Intriguingly, bacterial species commonly associated in high abundance with eukaryotic hosts include sphingolipid producers, such as the Bacteroidetes in the mammalian gut. To date, a role for bacterial sphingolipids in immune system maturation has been described, but their fate and impact in host physiology and metabolism remain to be elucidated...
January 9, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29328918/transmembrane-pickets-connect-cyto-and-pericellular-skeletons-forming-barriers-to-receptor-engagement
#20
Spencer A Freeman, Anthony Vega, Magdalena Riedl, Richard F Collins, Phillip P Ostrowski, Elliot C Woods, Carolyn R Bertozzi, Markku I Tammi, Diane S Lidke, Pauline Johnson, Satyajit Mayor, Khuloud Jaqaman, Sergio Grinstein
Phagocytic receptors must diffuse laterally to become activated upon clustering by multivalent targets. Receptor diffusion, however, can be obstructed by transmembrane proteins ("pickets") that are immobilized by interacting with the cortical cytoskeleton. The molecular identity of these pickets and their role in phagocytosis have not been defined. We used single-molecule tracking to study the interaction between Fcγ receptors and CD44, an abundant transmembrane protein capable of indirect association with F-actin, hence likely to serve as a picket...
January 11, 2018: Cell
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