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https://www.readbyqxmd.com/read/28727895/how-to-become-a-killer-or-is-it-all-accidental-virulence-strategies-in-oral-streptococci
#1
Izabela Sitkiewicz
Streptococci are a diverse group of gram positive microorganisms sharing common virulence traits and similar strategies to escape the oral niche and establish an infection in other parts of the host organism. Invasive infection with oral streptococci is "a perfect storm" that requires the concerted action of multiple biotic and abiotic factors. Our understanding of streptococcal pathogenicity and infectivity should probably be less mechanistic and driven not only by the identification of novel virulence factors...
July 20, 2017: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/28724888/crosscheck-an-open-source-web-tool-for-high-throughput-screen-data-analysis
#2
Jamil Najafov, Ayaz Najafov
Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28722347/foxo3-longevity-interactome-on-chromosome-6
#3
Timothy A Donlon, Brian J Morris, Randi Chen, Kamal H Masaki, Richard C Allsopp, D Craig Willcox, Ayako Elliott, Bradley J Willcox
FOXO3 has been implicated in longevity in multiple populations. By DNA sequencing in long-lived individuals, we identified all single nucleotide polymorphisms (SNPs) in FOXO3 and showed 41 were associated with longevity. Thirteen of these had predicted alterations in transcription factor binding sites. Those SNPs appeared to be in physical contact, via RNA polymerase II binding chromatin looping, with sites in the FOXO3 promoter, and likely function together as a cis-regulatory unit. The SNPs exhibited a high degree of LD in the Asian population, in which they define a specific longevity haplotype that is relatively common...
July 19, 2017: Aging Cell
https://www.readbyqxmd.com/read/28721506/interaction-between-a-bacterivorous-ciliate-aspidisca-cicada-and-a-rotifer-lecane-inermis-doozers-and-fraggles-in-aquatic-flocs
#4
Aleksandra Walczyńska, Mateusz Sobczyk, Edyta Fiałkowska, Agnieszka Pajdak-Stós, Janusz Fyda, Krzysztof Wiąckowski
Activated sludge is a semi-natural habitat composed of macroaggregates made by flocculating bacteria and inhabited by numerous protozoans and metazoans, creating a complicated interactome. The activated sludge resembles the biological formation of naturally occurring floc habitats, such as "marine snow." So far, these two types of habitat have been analyzed separately, despite their similarities. We examined the effect of a bacterivorous ciliate, Aspidisca cicada, on the quality of the macroaggregate ecosystem by estimating (i) the floc characteristics, (ii) the proliferation of other bacterivores (rotifers), and (iii) the chemical processes...
July 19, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#5
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28718811/tissue-specific-labeling-in-proteomics
#6
REVIEW
Evelyn Ramberger, Gunnar Dittmar
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed...
July 18, 2017: Proteomes
https://www.readbyqxmd.com/read/28718761/the-human-cytoplasmic-dynein-interactome-reveals-novel-activators-of-motility
#7
Willam B Redwine, Morgan E DeSantis, Ian Hollyer, Zaw Min Htet, Phuoc Tien Tran, Selene K Swanson, Laurence Florens, Michael P Washburn, Samara L Reck-Peterson
In human cells, cytoplasmic dynein-1 is essential for long-distance transport of many cargos, including organelles, RNAs, proteins, and viruses, towards microtubule minus ends. To understand how a single motor achieves cargo specificity, we identified the human dynein interactome by attaching a promiscuous biotin ligase ("BioID") to seven components of the dynein machinery, including a subunit of the essential cofactor dynactin. This method reported spatial information about the large cytosolic dynein/dynactin complex in living cells...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28716898/tbk1-provides-context-selective-support-of-the-activated-akt-mtor-pathway-in-lung-cancer
#8
Jonathan M Cooper, Yi-Hung Ou, Elizabeth McMillan, Rachel M Vaden, Aubhishek Zaman, Brian O Bodemann, Gurbani Makkar, Bruce A Posner, Michael White
Emerging observations link dysregulation of TANK-binding kinase 1 (TBK1) to developmental disorders, inflammatory disease, and cancer. Biochemical mechanisms accounting for direct participation of TBK1 in host defense signaling have been well described. However, the molecular underpinnings of the selective participation of TBK1 in a myriad of additional cell biological systems in normal and pathophysiological contexts remain poorly understood. To elucidate the context-selective role of TBK1 in cancer cell survival, we employed a combination of broad-scale chemogenomic and interactome discovery strategies to generate data-driven mechanism-of-action hypotheses...
July 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28716126/the-effects-of-potato-virus-y-derived-virus-small-interfering-rnas-of-three-biologically-distinct-strains-on-potato-solanum-tuberosum-transcriptome
#9
Lindani Moyo, Shunmugiah V Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, Hanu R Pappu
BACKGROUND: Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions...
July 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/28715999/factors-affecting-interactome-based-prediction-of-human-genes-associated-with-clinical-signs
#10
Sara González-Pérez, Florencio Pazos, Mónica Chagoyen
BACKGROUND: Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28713243/synaptic-interactome-mining-reveals-p140cap-as-a-new-hub-for-psd-proteins-involved-in-psychiatric-and-neurological-disorders
#11
Annalisa Alfieri, Oksana Sorokina, Annie Adrait, Costanza Angelini, Isabella Russo, Alessandro Morellato, Michela Matteoli, Elisabetta Menna, Elisabetta Boeri Erba, Colin McLean, J Douglas Armstrong, Ugo Ala, Joseph D Buxbaum, Alfredo Brusco, Yohann Couté, Silvia De Rubeis, Emilia Turco, Paola Defilippi
Altered synaptic function has been associated with neurological and psychiatric conditions including intellectual disability, schizophrenia and autism spectrum disorder (ASD). Amongst the recently discovered synaptic proteins is p140Cap, an adaptor that localizes at dendritic spines and regulates their maturation and physiology. We recently showed that p140Cap knockout mice have cognitive deficits, impaired long-term potentiation (LTP) and long-term depression (LTD), and immature, filopodia-like dendritic spines...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28713027/an-on-matrix-digestion-procedure-for-ap-ms-experiments-dissects-the-interplay-between-complex-conserved-and-serotype-specific-reactivities-in-dengue-virus-human-plasma-interactome
#12
Yassel Ramos, Vivian Huerta, Dayron Martín, Sucel Palomares, Alexis Yero, Dianne Pupo, Sebastien Gallien, Alejandro M Martín, Yasset Pérez-Riverol, Mónica Sarría, Osmany Guirola, Glay Chinea, Bruno Domon, Luis Javier González
The interactions between the four Dengue virus (DENV) serotypes and plasma proteins are crucial in the initial steps of viral infection to humans. Affinity purification combined with quantitative mass spectrometry analysis, has become one of the most powerful tools for the investigation on novel protein-protein interactions. Using this approach, we report here that a significant number of bait-interacting proteins do not dissociate under standard elution conditions, i.e. acid pH and chaotropic agents, and that this problem can be circumvented by using the "on-matrix" digestion procedure described here...
July 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28712724/acylglycerol-kinase-mutated-in-sengers-syndrome-is-a-subunit-of-the-tim22-protein-translocase-in-mitochondria
#13
Milena Vukotic, Hendrik Nolte, Tim König, Shotaro Saita, Maria Ananjew, Marcus Krüger, Takashi Tatsuta, Thomas Langer
Mutations in mitochondrial acylglycerol kinase (AGK) cause Sengers syndrome, which is characterized by cataracts, hypertrophic cardiomyopathy, and skeletal myopathy. AGK generates phosphatidic acid and lysophosphatidic acid, bioactive phospholipids involved in lipid signaling and the regulation of tumor progression. However, the molecular mechanisms of the mitochondrial pathology remain enigmatic. Determining its mitochondrial interactome, we have identified AGK as a constituent of the TIM22 complex in the mitochondrial inner membrane...
July 8, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28712289/comprehensive-proteomic-analysis-of-pgc7-interacting-proteins
#14
Liu Hongliang, Zhang Lei, Wei Qing, Shi Zhaopeng, Shi Xiaoyan, Du Juan, Huang Chenyang, Zhang Yong, Guo Zekun
Primordial germ cell 7 (PGC7), a maternal factor essential for early development, plays a critical role in the regulation of DNA methylation, transcriptional repression, chromatin condensation, and cell division and the maintenance of cell pluripotentiality. Despite the fundamental roles of PGC7 in these cellular processes, only a few molecular and functional interactions of PGC7 have been reported. Here, a streptavidin-biotin affinity purification technique combined with LC-MS/MS was used to analyze potential proteins that interact with PGC7...
July 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28710492/nek1-kinase-domain-structure-and-its-dynamic-protein-interactome-after-exposure-to-cisplatin
#15
Talita D Melo-Hanchuk, Priscila Ferreira Slepicka, Gabriela Vaz Meirelles, Fernanda Luisa Basei, Diogo Ventura Lovato, Daniela Campos Granato, Bianca Alves Pauletti, Romenia Ramos Domingues, Adriana Franco Paes Leme, Alessandra Luiza Pelegrini, Guido Lenz, Stefan Knapp, Jonathan M Elkins, Jörg Kobarg
NEK family kinases are serine/threonine kinases that have been functionally implicated in the regulation of the disjunction of the centrosome, the assembly of the mitotic spindle, the function of the primary cilium and the DNA damage response. NEK1 shows pleiotropic functions and has been found to be mutated in cancer cells, ciliopathies such as the polycystic kidney disease, as well as in the genetic diseases short-rib thoracic dysplasia, Mohr-syndrome and amyotrophic lateral sclerosis. NEK1 is essential for the ionizing radiation DNA damage response and priming of the ATR kinase and of Rad54 through phosphorylation...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710009/mrna-interactome-capture-in-mammalian-cells
#16
Nicolai Kastelic, Markus Landthaler
Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28707887/full-characterization-of-localization-diversity-in-human-protein-interactome
#17
Lixin Cheng, Kaili Fan, Yan Huang, Dong Wang, Kwong-Sak Leung
Spatial-temporal regulation amongst proteins forms dynamic networks in cells. Co-existence in common cell compartments can improve biological reliability of the protein-protein interactions. However, this is usually overlooked by most proteomic studies and leads to unrealistic discoveries. In this paper, we systematically characterize the interaction localization diversity in human protein interactome using localization coefficient, a novel metric proposed for assessing how diversely the interactions localize among cell compartments...
July 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28706229/quantitative-interactome-of-a-membrane-bcl-2-network-identifies-a-hierarchy-of-complexes-for-apoptosis-regulation
#18
Stephanie Bleicken, Annika Hantusch, Kushal Kumar Das, Tancred Frickey, Ana J Garcia-Saez
The Bcl-2 proteins form a complex interaction network that controls mitochondrial permeabilization and apoptosis. The relative importance of different Bcl-2 complexes and their spatio-temporal regulation is debated. Using fluorescence cross-correlation spectroscopy to quantify the interactions within a minimal Bcl-2 network, comprised by cBid, Bax, and Bcl-xL, we show that membrane insertion drastically alters the pattern of Bcl-2 complexes, and that the C-terminal helix of Bcl-xL determines its binding preferences...
July 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28706196/synaptic-gap-and-gef-complexes-cluster-proteins-essential-for-gtp-signaling
#19
Brent Wilkinson, Jing Li, Marcelo P Coba
GTPase-activating proteins (GAPs) and guanine exchange factors (GEFs) play essential roles in regulating the activity of small GTPases. Several GAPs and GEFs have been shown to be present at the postsynaptic density (PSD) within excitatory glutamatergic neurons and regulate the activity of glutamate receptors. However, it is not known how synaptic GAP and GEF proteins are organized within the PSD signaling machinery, if they have overlapping interaction networks, or if they associate with proteins implicated in contributing to psychiatric disease...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28704418/the-coll%C3%AE-gen-iii-fibril-has-a-flexi-rod-structure-of-flexible-sequences-interspersed-with-rigid-bioactive-domains-including-two-with-hemostatic-roles
#20
J Des Parkin, James D San Antonio, Anton V Persikov, Hayat Dagher, Raymond Dalgleish, Shane T Jensen, Xavier Jeunemaitre, Judy Savige
Collagen III is critical to the integrity of blood vessels and distensible organs, and in hemostasis. Examination of the human collagen III interactome reveals a nearly identical structural arrangement and charge distribution pattern as for collagen I, with cell interaction domains, fibrillogenesis and enzyme cleavage domains, several major ligand-binding regions, and intermolecular crosslink sites at the same sites. These similarities allow heterotypic fibril formation with, and substitution by, collagen I in embryonic development and wound healing...
2017: PloS One
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