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https://www.readbyqxmd.com/read/29786716/unexpected-protonation-state-of-glu197-discovered-from-simulations-of-tacrine-in-butyrylcholinesterase
#1
Xiao Wan, Yuan Yao, Lei Fang, Junjun Liu
Butyrylcholinesterase (BChE) has been actively involved in drug discoveries from many fields for decades. In the crystal structure of the BChE-tacrine complex, there is an unanticipated formyl-proline molecule resolved very close to tacrine, raising an essential question on how reliable it is to apply the binding pose in a crystal structure to analyze related experimental observations, in which no formyl-proline is actually involved. In this study, by performing a series of 100 ns molecular dynamics simulations, we demonstrate that it is safe to employ the structural information from this crystal structure to analyze related experimental observations...
May 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29786505/can-pallars-i-llobateres-a-new-hominoid-bearing-locality-from-the-late-miocene-of-the-vall%C3%A3-s-pened%C3%A3-s-basin-ne-iberian-peninsula
#2
David M Alba, Isaac Casanovas-Vilar, Marc Furió, Israel García-Paredes, Chiara Angelone, Sílvia Jovells-Vaqué, Àngel H Luján, Sergio Almécija, Salvador Moyà-Solà
In the Iberian Peninsula, Miocene apes (Hominoidea) are generally rare and mostly restricted to the Vallès-Penedès Basin. Here we report a new hominoid maxillary fragment with M2 from this basin. It was surface-collected in March 2017 from the site of Can Pallars i Llobateres (CPL, Sant Quirze del Vallès), where fossil apes had not been previously recorded. The locality of provenance (CPL-M), which has delivered no further fossil remains, is located very close (ca. 50 m) to previously known CPL outcrops, and not very far (ca...
May 18, 2018: Journal of Human Evolution
https://www.readbyqxmd.com/read/29786414/uncovering-the-design-principle-of-amino-acid-derived-photoluminescent-bio-dots-with-tailored-made-structure-properties-and-application-for-cellular-bioimaging
#3
Hesheng Victor Xu, Xinting Zheng, Yanli Zhao, Yen Nee Tan
Natural amino acids possess side chains with different functional groups (R groups), which make them excellent precursors for programmable synthesis of biomolecule-derived nanodots (bio-dots) with desired properties. Herein, we reported the first systematic study to uncover the material design rules of bio-dots synthesis from 20 natural α-amino acids via a green hydrothermal approach. The as-synthesized amino acids bio-dots (AA-dots) are comprehensively characterised to establish a structure-properties relationship between the amino acid precursors and the corresponding photoluminescent properties of AA-dots...
May 22, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29786170/immunopeptidomic-profiling-of-hla-a2-positive-triple-negative-breast-cancer-identifies-potential-immunotherapy-target-antigens
#4
Nicola Ternette, Marloes J M Olde Nordkamp, Julius Muller, Amanda P Anderson, Annalisa Nicastri, Adrian V S Hill, Benedikt M Kessler, Demin Li
The recent development in immune checkpoint inhibitors and chimeric antigen receptor (CAR) T-cells in the treatment of cancer has not only demonstrated the potency of utilising T-cell reactivity for cancer therapy, but has also highlighted the need for developing new approaches to discover targets suitable for such novel therapeutics. Here we analysed the immunopeptidomes of 6 HLA-A2-positive triple negative breast cancer (TNBC) samples by nano-ultra performance liquid chromatography tandem mass spectrometry (nUPLC-MS2 )...
May 22, 2018: Proteomics
https://www.readbyqxmd.com/read/29786147/timing-and-frequency-of-sublethal-exposure-modifies-the-induction-and-retention-of-increased-insecticide-tolerance-in-wood-frogs-lithobates-sylvaticus
#5
Devin K Jones, Erika K Yates, Brian M Mattes, William D Hintz, Matthew S Schuler, Rick A Relyea
While the paradigm for increased tolerance to pesticides has been by selection on constitutive (naïve) traits, recent research has shown it can also occur through phenotypic plasticity. However, the time period in which induction can occur, the duration of induced tolerance, and the influence of multiple induction events remain unknown. We hypothesized that the induction of increased pesticide tolerance is limited to early sensitive periods, the magnitude of induced tolerance depends on the number of exposures, and the retention of induced tolerance depends on the time elapsed after an exposure and the number of exposures...
May 22, 2018: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/29786092/mapping-the-physical-network-of-cellular-interactions
#6
Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J Muraro, Anna Lyubimova, Alexander van Oudenaarden
A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1+ enteroendocrine cell-Lgr5+ stem cell interaction in small intestine crypts...
May 21, 2018: Nature Methods
https://www.readbyqxmd.com/read/29785586/suicide-by-plastic-bag-suffocation-combined-with-the-mixture-of-citric-acid-and-baking-soda-in-an-adolescent
#7
Keishu Murakami, Takashi Kawaguchi, Yumiko Hashizume, Kengo Kitamura, Misato Okada, Kohei Okumoto, Shoich Sakamoto, Yuko Ishida, Mizuho Nosaka, Akihiko Kimura, Akihiro Takatsu, Toshikazu Kondo
We describe a case of suicidal asphyxiation using a plastic bag combined with carbon dioxide (CO2 ) gas. A 20-year-old male, whose head was covered with a plastic bag, was found dead in his room. In the plastic bag, there were two glass-made cups containing liquid-like substance. Through crime scene investigation by police staffs, a bottle of citric acid and a box of baking soda were also discovered in his room. The forensic autopsy revealed that there were neither lesions nor injuries in all of the organs...
May 22, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29785461/clinical-significance-of-appendiceal-diverticulum-a-significant-marker-for-appendiceal-neoplasia-in-australian-patients
#8
Daniel Leonard Chan, Christopher Lim, Arsalan Bakhtiar, Matthew Khoury, Michelle Smigelski, Dean Yeh, Praveen Ravindran
INTRODUCTION: Diverticula of the appendix (DA) have a reported incidence of up to 2.1%. They are primarily detected incidentally, through imaging and intraoperative or histologic diagnosis. This study's objective was to examine the prevalence of DA, and its relationship with inflammation and neoplasia, as well as review the literature with respect to clinical outcomes and ability to identify DA preoperatively. METHODOLOGY: A retrospective search of all patients undergoing an appendicectomy for right lower quadrant pain at a single institution between 2004 and 2017 was conducted...
May 21, 2018: International Journal of Colorectal Disease
https://www.readbyqxmd.com/read/29785343/perinatal-specimens-of-maiasaura-from-the-upper-cretaceous-of-montana-usa-insights-into-the-early-ontogeny-of-saurolophine-hadrosaurid-dinosaurs
#9
Albert Prieto-Marquez, Merrilee F Guenther
Perinatal specimens of hadrosaurids discovered in the late 1970's by field crews from Princeton University were significant in providing evidence of the early ontogenetic stages in North American dinosaurs. These specimens from the Campanian (Upper Cretaceous) Two Medicine Formation of Montana consist of over a dozen skeletons referable to the saurolophine hadrosaurid Maiasaura peeblesorum , but never fully figured or described. Here, we provide a more complete documentation of the morphology of these specimens, along with an examination of variation during a large span of the development of saurolophine hadrosaurids...
2018: PeerJ
https://www.readbyqxmd.com/read/29785273/gene-regulation-associated-with-sexual-development-and-female-fertility-in-different-isolates-of-trichoderma-reesei
#10
Christoph Dattenböck, Doris Tisch, Andre Schuster, Alberto Alonso Monroy, Wolfgang Hinterdobler, Monika Schmoll
Background: Trichoderma reesei is one of the most frequently used filamentous fungi in industry for production of homologous and heterologous proteins. The ability to use sexual crossing in this fungus was discovered several years ago and opens up new perspectives for industrial strain improvement and investigation of gene regulation. Results: Here we investigated the female sterile strain QM6a in comparison to the fertile isolate CBS999.97 and backcrossed derivatives of QM6a, which have regained fertility (FF1 and FF2 strains) in both mating types under conditions of sexual development...
2018: Fungal Biology and Biotechnology
https://www.readbyqxmd.com/read/29785216/-staphylococcus-aureus-surface-protein-g-is-an-immunodominant-protein-and-a-possible-target-in-an-anti-biofilm-drug-development
#11
Yury Belyi, Ivan Rybolovlev, Nikita Polyakov, Alena Chernikova, Irina Tabakova, Alexandre Gintsburg
Background: Staphylococcus aureus is a Gram-positive bacterium that causes severe illnesses in the human population. The capacity of S. aureus strains to form biofilms on biotic and abiotic surfaces creates serious problems for treatment of hospital infections and has stimulated efforts to develop new means of specific protection or immunotherapy. Material and Methods: We found that rabbit serum raised against crude concentrated S. aureus liquid culture significantly decreased the development of staphylococcal biofilm in vitro ...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#12
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29785052/observation-of-anisotropic-magneto-peltier-effect-in-nickel
#13
Ken-Ichi Uchida, Shunsuke Daimon, Ryo Iguchi, Eiji Saitoh
The Peltier effect, discovered in 1834, converts a charge current into a heat current in a conductor, and its performance is described by the Peltier coefficient, which is defined as the ratio of the generated heat current to the applied charge current1,2 . To exploit the Peltier effect for thermoelectric cooling or heating, junctions of two conductors with different Peltier coefficients have been believed to be indispensable. Here we challenge this conventional wisdom by demonstrating Peltier cooling and heating in a single material without junctions...
May 21, 2018: Nature
https://www.readbyqxmd.com/read/29784946/interpretable-dimensionality-reduction-of-single-cell-transcriptome-data-with-deep-generative-models
#14
Jiarui Ding, Anne Condon, Sohrab P Shah
Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data...
May 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29784881/structural-basis-for-adp-dependent-glucokinase-inhibition-by-8-bromo-substituted-adenosine-nucleotide
#15
Przemyslaw Grudnik, Marcin M Kaminski, Krzysztof P Rembacz, Katarzyna Kuska, Mariusz Madej, Jan Potempa, Maciej Dawidowski, Grzegorz Dubin
In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose-6-phosphate. In contrast to canonical hexokinases which use ATP, ADP-dependent glucokinase (ADPGK) catalyzes non-canonical phosphorylation of glucose to glucose-6-phosphate using ADP as a phosphate donor. Initially discovered in Archaea, the human homolog of ADPGK was described only recently. ADPGK's involvement in modified bioenergetics of activated T cells has been postulated and elevated ADPGK expression has been reported in various cancer tissues...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784874/select-%C3%AE-arrestins-control-cell-surface-abundance-of-the-mammalian-kir2-1-potassium-channel-in-a-yeast-model
#16
Natalie A Hager, Collin J Krasowski, Timothy D Mackie, Alexander R Kolb, Patrick G Needham, Andrew A Augustine, Alison Dempsey, Christopher Szent-Gyorgyi, Marcel P Bruchez, Daniel J Bain, Adam V Kwiatkowski, Allyson F O'Donnell, Jeffrey L Brodsky
Protein composition at the plasma membrane is tightly regulated, with rapid protein internalization and selective targeting to the cell surface occurring in response to environmental changes. For example, ion channels are dynamically relocalized to or from the plasma membrane in response to physiological alterations, allowing cells and organisms to maintain osmotic and salt homeostasis. To identify additional factors that regulate the selective trafficking of a specific ion channel, we used a yeast model for a mammalian potassium channel, the K+ inwardly rectifying channel Kir2...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784847/translation-elongation-factor-4-lepa-contributes-to-tetracycline-susceptibility-by-stalling-elongating-ribosomes
#17
Bin Liu, Chunlai Chen
Even though elongation factor 4 (EF4) is the third most conserved protein in bacteria, its physiological functions remain largely unknown and its proposed molecular mechanisms are conflicting among previous studies. In the present study we show that growth of an Escherichia coli strain is more susceptible to tetracycline than its EF4 knockout strain. In consistence with previous studies, our results suggested that EF4 affects ribosome biogenesis when tetracycline is present. Through ribosome profiling analysis, we discovered that EF4 causes 1-nucleotide shifting of ribosomal footprints on mRNA when cells have been exposed to tetracycline...
May 21, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29784762/discovering-the-cause-of-wiskott-aldrich-syndrome-and-laying-the-foundation-for-understanding-immune-cell-structuring
#18
Emily M Mace, Jordan S Orange
No abstract text is available yet for this article.
June 1, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29784711/quantitative-proteome-and-phosphoproteome-analyses-of-streptomyces-coelicolor-reveal-proteins-and-phosphoproteins-modulating-differentiation-and-secondary-metabolism
#19
Beatriz Rioseras, Pavel V Sliaha, Vladimir Gorshkov, Paula Yagüe, Maria T López-García, Nathaly González-Quiñónez, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Ole N Jensen, Angel Manteca
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode a large number of Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor...
May 21, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29784696/why-are-we-failing-to-address-the-issue-of-access-to-insulin-a-national-and-global-perspective
#20
David Beran, Irl B Hirsch, John S Yudkin
Insulin was discovered in 1921 and soon became widely available in high-income countries. However, many people currently in need of this life-saving medicine are unable to access it. This is a global phenomenon, impacting not only populations of low- and middle-income countries but low-income populations in the U.S. In the U.S., the rate of diabetic ketoacidosis remains high in certain subpopulations, the cost of insulin being the main precipitating factor. On a global level the main cause of mortality for a child with type 1 diabetes is a lack of access to insulin, and in sub-Saharan Africa the life expectancy of a child with type 1 diabetes can be as low as 1 year...
June 2018: Diabetes Care
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