keyword
https://read.qxmd.com/read/36674791/proximity-mapping-of-ccp6-reveals-its-association-with-centrosome-organization-and-cilium-assembly
#21
JOURNAL ARTICLE
Sergi Rodriguez-Calado, Petra Van Damme, Francesc Xavier Avilés, Ana Paula Candiota, Sebastian Tanco, Julia Lorenzo
The cytosolic carboxypeptidase 6 (CCP6) catalyzes the deglutamylation of polyglutamate side chains, a post-translational modification that affects proteins such as tubulins or nucleosome assembly proteins. CCP6 is involved in several cell processes, such as spermatogenesis, antiviral activity, embryonic development, and pathologies like renal adenocarcinoma. In the present work, the cellular role of CCP6 has been assessed by BioID, a proximity labeling approach for mapping physiologically relevant protein-protein interactions (PPIs) and bait proximal proteins by mass spectrometry...
January 9, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/36552604/mangosteen-pericarp-extract-supplementation-boosts-antioxidant-status-via-rebuilding-gut-microbiota-to-attenuate-motor-deficit-in-6-ohda-induced-parkinson-s-disease
#22
JOURNAL ARTICLE
Bira Arumndari Nurrahma, Tu-Hsueh Yeh, Rong-Hong Hsieh, Shu-Ping Tsao, Chia-Wen Chen, Yen-Peng Lee, Chun-Hsu Pan, Hui-Yu Huang
Oxidative stress and gut dysbiosis have been known to precede Parkinson's disease (PD). An antioxidant-rich product, mangosteen pericarp (MP), has the ability to counterbalance excessive free radicals and the imbalanced gut microbiota composition, suggesting the MP's capacity to delay PD progression. In this study, we explored the effects of two doses of MP extract in a unilateral 6-hydroxydopamine (6-OHDA)-induced PD rat model. We revealed that the 8-week supplementation of a low dose (LMP) and a high dose of the MP extract (HMP) improved motor function, as observed in decreased contralateral rotation, improved time spent on rod, and higher dopamine binding transporter (DAT) in the substantia nigra pars compacta (SNc)...
December 2, 2022: Antioxidants (Basel, Switzerland)
https://read.qxmd.com/read/36478633/molecular-methods-to-study-protein-trafficking-between-organs
#23
REVIEW
Felix K Kreissl, Michael A Banki, Ilia A Droujinine
Interorgan communication networks are key regulators of organismal homeostasis, and their dysregulation is associated with a variety of pathologies. While mass spectrometry proteomics identifies circulating proteins and can correlate their abundance with disease phenotypes, the tissues of origin and destinations of these secreted proteins remain largely unknown. approaches to study protein secretion are valuable, however, they may not mimic the complexity of in environments. More recently, the development of engineered promiscuous BirA* biotin ligase derivatives has enabled tissue-specific tagging of cellular secreted proteomes in vivo...
December 7, 2022: Proteomics
https://read.qxmd.com/read/36446975/sumo-id-a-strategy-for-the-identification-of-sumo-dependent-proximal-interactors
#24
JOURNAL ARTICLE
Orhi Barroso-Gomila, Ugo Mayor, Rosa Barrio, James D Sutherland
Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its non-covalent interaction with SUMO-interacting motifs (SIMs) found in some proteins. Investigating such partner-complex formation is particularly challenging due to the fast dynamics and reversibility of SUMO modifications and the low affinity of SUMO-SIM interactions...
2023: Methods in Molecular Biology
https://read.qxmd.com/read/36437406/clk1-clk2-driven-signalling-at-the-leishmania-kinetochore-is-captured-by-spatially-referenced-proximity-phosphoproteomics
#25
JOURNAL ARTICLE
Vincent Geoghegan, Juliana B T Carnielli, Nathaniel G Jones, Manuel Saldivia, Sergios Antoniou, Charlotte Hughes, Rachel Neish, Adam Dowle, Jeremy C Mottram
Kinetochores in the parasite Leishmania and related kinetoplastids appear to be unique amongst eukaryotes and contain protein kinases as core components. Using the kinetochore kinases KKT2, KKT3 and CLK2 as baits, we developed a BirA* proximity biotinylation methodology optimised for sensitivity, XL-BioID, to investigate the composition and function of the Leishmania kinetochore. We could detect many of the predicted components and also discovered two novel kinetochore proteins, KKT24 and KKT26. Using KKT3 tagged with a fast-acting promiscuous biotin ligase variant, we took proximity biotinylation snapshots of the kinetochore in synchronised parasites...
November 28, 2022: Communications Biology
https://read.qxmd.com/read/36423023/hepatitis-b-c-and-d-virus-infection-among-population-aged-10-64-years-in-mongolia-baseline-survey-data-of-a-nationwide-cancer-cohort-study
#26
JOURNAL ARTICLE
Davaalkham Dambadarjaa, Otgonbayar Radnaa, Ser-Od Khuyag, Oyu-Erdene Shagdarsuren, Uranbaigali Enkhbayar, Yerkyebulan Mukhtar, Enkh-Oyun Tsogzolbaatar, Gunchmaa Nyam, Shatar Shaarii, Pramil Singh, Masaharu Takahashi, Bira Namdag, Hiroaki Okamoto
Hepatitis B, C, and D virus infections are a major public health problem, and Mongolia has one of the highest prevalences of dual and triple infections in the world. We aimed to determine the seroprevalence of hepatitis infection and dual or triple hepatitis infections among 10-64-year-olds. A questionnaire was used to identify risk factors for hepatitis infection, and seromarkers were measured by the fully automated immunologic analyzer HISCL-5000. Among a total of 10,040 participants, 8.1% of the population aged 10-64 was infected with HBV, 9...
November 14, 2022: Vaccines
https://read.qxmd.com/read/36309084/a-novel-connection-between-trypanosoma-brucei-mitochondrial-proteins-tbtim17-and-tbtrap1-is-discovered-using-biotinylation-identification-bioid
#27
JOURNAL ARTICLE
Fidel Soto-Gonzalez, Anuj Tripathi, Ayorinde Cooley, Victor Paromov, Tanu Rana, Minu Chaudhuri
The protein translocase of the mitochondrial inner membrane in Trypanosoma brucei, TbTIM17, forms a modular complex in association with several other trypanosome-specific proteins. To identify transiently interacting proximal partner(s) of TbTim17, we used Biotinylation Identification (BioID) by expressing a modified biotin ligase-TbTim17 (BirA*-TbTim17) fusion protein in T. brucei. BirA*-TbTim17 was targeted to mitochondria and assembled in the TbTIM complex. In the presence of biotin, BirA*-TbTim17 biotinylated several mitochondrial proteins...
October 26, 2022: Journal of Biological Chemistry
https://read.qxmd.com/read/36267337/synophtalmia-on-a-newborn
#28
Laetitia Bihamba Bira, Franck Katembo Sikakulya, Mupenzi Mumbere, Jeff Mathe
Synophtalmia or cyclopia is a rare presentation of alobar holoprosencephaly. Cases which have been reported are stillborn or dead in post-delivery period. We are presenting a 3000-g live full-term newborn girl delivered by caesarean section with a well-marked cyclopia, but who died 30 min post-delivery. The case did not present with other abnormalities. The literature showed that genetic disorders are associated with cyclopia. A prenatal anomaly scan can help in the early detection of the condition and timely termination of the pregnancy can be conducted...
2022: SAGE Open Medical Case Reports
https://read.qxmd.com/read/36205702/proteomic-and-phosphoproteomic-analyses-reveal-the-oncogenic-role-of-ptk7-ndrg1-axis-in-non-small-cell-lung-cancer-cell-resistance-to-azd9291
#29
JOURNAL ARTICLE
Zhen Wang, Panpan Lei, Ziyang Li, Xiao Han, Fei Yang, Tian Su, Caiting Meng, Zhanwu Hou, Huadong Liu
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are the most important chemotherapeutics for non-small-cell lung cancer (NSCLC) therapy. The resistance to EGFR-TKIs is one of the biggest obstacles to NSCLC outcome. In this study, taking advantage of phospho- and proximal proteomic techniques, we analyzed the network rearrangement in cell lines responding to AZD9291 treatment and found that cell-cell adhesion was dramatically enhanced in AZD9291-resistant cells. Further analysis revealed that protein tyrosine kinase 7 (PTK7) expression was significantly elevated...
October 7, 2022: ACS Chemical Biology
https://read.qxmd.com/read/36190279/airid-based-proximity-labeling-for-protein-protein-interaction-in-plants
#30
JOURNAL ARTICLE
Ahmad Zada, Imran Khan, Min Zhang, Yuting Cheng, Xueyun Hu
In mammalian cells and plants, proximity labeling (PL) approaches using modified ascorbate peroxidase (APEX) or the Escherichia coli biotin ligase BirA (known as BioID) have proven successful in identifying protein-protein interactions (PPIs). APEX, BioID, and TurboID, a revised version of BioID have some restrictions in addition to being valuable technologies. The recently developed AirID, a novel version of BioID for proximity identification in protein-protein interactions, overcame these restrictions. Previously, AirID has been used in animal models, while the current study demonstrates the use of AirID in plants, and the results confirmed that AirID performs better in plant systems as compared to other PL enzymes such as BioID and TurboID for protein labeling that are proximal to the target proteins...
September 16, 2022: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/36084055/an-open-source-low-cost-voluntary-running-activity-tracking-tool-for-in-vivo-rodent-studies
#31
JOURNAL ARTICLE
Grace E Deitzler, Nicholas P Bira, Joseph R Davidson, Maude M David
In vivo rodent behavioral and physiological studies often benefit from measurement of general activity. However, many existing instruments necessary to track such activity are high in cost and invasive within home cages, some even requiring extensive separate cage systems, limiting their widespread use to collect data. We present here a low-cost open-source alternative that measures voluntary wheel running activity and allows for modulation and customization, along with a reproducible and easy to set-up code pipeline for setup and analysis in Arduino IDE and R...
2022: PloS One
https://read.qxmd.com/read/36063330/tethering-complex-proteins-and-protein-complexes-for-optical-tweezers-experiments
#32
JOURNAL ARTICLE
Kevin Maciuba, Christian M Kaiser
Tethering proteins to force probes, typically micrometer-sized beads, is a prerequisite for dissecting their properties with optical tweezers. DNA handles serve as spacers between the tethered protein of interest and the bead surface. Attachment sites of the DNA handles to both the surface of beads and to the protein of interest must be mechanically stable for optical tweezers experiments. The most prominent method for attaching DNA handles to proteins utilizes thiol chemistry, linking modified DNA to engineered cysteines in the target protein...
2022: Methods in Molecular Biology
https://read.qxmd.com/read/35973513/proximity-labeling-of-endogenous-rictor-identifies-mtor-complex-2-regulation-by-adp-ribosylation-factor-arf1
#33
JOURNAL ARTICLE
Amelia K Luciano, Ekaterina Korobkina, Scott P Lyons, John A Haley, Shelagh Fluharty, Su Myung Jung, Arminja N Kettenbach, David A Guertin
Mechanistic Target of Rapamycin (mTOR) complex 2 (mTORC2) regulates metabolism, cell proliferation, and cell survival. mTORC2 activity is stimulated by growth factors, and it phosphorylates the hydrophobic motif site of the AGC kinases AKT, SGK, and PKC. However, the proteins that interact with mTORC2 to control its activity and localization remain poorly defined. To identify mTORC2 interacting proteins in living cells, we tagged endogenous RICTOR, an essential mTORC2 subunit, with the modified BirA biotin ligase BioID2 and performed live-cell proximity labeling...
August 13, 2022: Journal of Biological Chemistry
https://read.qxmd.com/read/35946312/a-genetic-model-for-in-vivo-proximity-labelling-of-the-mammalian-secretome
#34
JOURNAL ARTICLE
Rui Yang, Amanda S Meyer, Ilia A Droujinine, Namrata D Udeshi, Yanhui Hu, Jinjin Guo, Jill A McMahon, Dominique K Carey, Charles Xu, Qiao Fang, Jihui Sha, Shishang Qin, David Rocco, James Wohlschlegel, Alice Y Ting, Steven A Carr, Norbert Perrimon, Andrew P McMahon
Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a BirA*G3 mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway...
August 2022: Open Biology
https://read.qxmd.com/read/35937934/-in-vivo-characterization-of-endogenous-protein-interactomes-in-drosophila-larval-brain-using-a-crispr-cas9-based-strategy-and-bioid-based-proximity-labeling
#35
JOURNAL ARTICLE
Ezgi Uçkun, Georg Wolfstetter, Johannes Fuchs, Ruth H Palmer
Understanding protein-protein interactions (PPIs) and interactome networks is essential to reveal molecular mechanisms mediating various cellular processes. The most common method to study PPIs in vivo is affinity purification combined with mass spectrometry (AP-MS). Although AP-MS is a powerful method, loss of weak and transient interactions is still a major limitation. Proximity labeling (PL) techniques have been developed as alternatives to overcome these limitations. Proximity-dependent biotin identification (BioID) is one such widely used PL method...
July 5, 2022: Bio-protocol
https://read.qxmd.com/read/35788163/engineering-of-ultraid-a-compact-and-hyperactive-enzyme-for-proximity-dependent-biotinylation-in-living-cells
#36
JOURNAL ARTICLE
Lea Kubitz, Sebastian Bitsch, Xiyan Zhao, Kerstin Schmitt, Lukas Deweid, Amélie Roehrig, Elisa Cappio Barazzone, Oliver Valerius, Harald Kolmar, Julien Béthune
Proximity-dependent biotinylation (PDB) combined with mass spectrometry analysis has established itself as a key technology to study protein-protein interactions in living cells. A widespread approach, BioID, uses an abortive variant of the E. coli BirA biotin protein ligase, a quite bulky enzyme with slow labeling kinetics. To improve PDB versatility and speed, various enzymes have been developed by different approaches. Here we present a small-size engineered enzyme: ultraID. We show its practical use to probe the interactome of Argonaute-2 after a 10 min labeling pulse and expression at physiological levels...
July 4, 2022: Communications Biology
https://read.qxmd.com/read/35759281/cognitive-behavioral-therapy-for-veterans-with-comorbid-posttraumatic-headache-and-posttraumatic-stress-disorder-symptoms-a-randomized-clinical-trial
#37
RANDOMIZED CONTROLLED TRIAL
Donald D McGeary, Patricia A Resick, Donald B Penzien, Cindy A McGeary, Timothy T Houle, Blessen C Eapen, Carlos A Jaramillo, Paul S Nabity, David E Reed, John C Moring, Lindsay M Bira, Hunter R Hansen, Stacey Young-McCaughan, Briana A Cobos, Jim Mintz, Terence M Keane, Alan L Peterson
IMPORTANCE: Posttraumatic headache is the most disabling complication of mild traumatic brain injury. Posttraumatic stress disorder (PTSD) symptoms are often comorbid with posttraumatic headache, and there are no established treatments for this comorbidity. OBJECTIVE: To compare cognitive behavioral therapies (CBTs) for headache and PTSD with treatment per usual (TPU) for posttraumatic headache attributable to mild traumatic brain injury. DESIGN, SETTING, AND PARTICIPANTS: This was a single-site, 3-parallel group, randomized clinical trial with outcomes at posttreatment, 3-month follow-up, and 6-month follow-up...
August 1, 2022: JAMA Neurology
https://read.qxmd.com/read/35688383/microid2-a-novel-biotin-ligase-enables-rapid-proximity-dependent-proteomics
#38
JOURNAL ARTICLE
Benjamin S Johnson, Lexie Chafin, Daniela Farkas, Jessica Adair, Ajit Elhance, Laszlo Farkas, Joseph S Bednash, James D Londino
Identifying protein-protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity dependent biotinylation method that uses an "abortive" biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist...
June 7, 2022: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/35601102/tag-thy-neighbour-nanometre-scale-insights-into-kinetoplastid-parasites-with-proximity-dependent-biotinylation
#39
REVIEW
Vincent Geoghegan, Jeremy C Mottram, Nathaniel G Jones
Proximity labelling is a powerful and rapidly developing technology for exploring the interaction space and molecular environment of a protein of interest at the nanometre scale. In proximity labelling, a promiscuous biotinylating enzyme is genetically fused to the protein of interest, initiation of labelling then results in the biotinylating enzyme generating reactive biotin which covalently 'tags' nearby molecules. Importantly, this labelling takes place in vivo whilst the protein of interest continues to perform its normal functions in the cell...
2022: Frontiers in Cellular and Infection Microbiology
https://read.qxmd.com/read/35591235/development-of-the-romanian-radar-sensor-for-space-surveillance-and-tracking-activities
#40
JOURNAL ARTICLE
Liviu Ionescu, Alexandru Rusu-Casandra, Calin Bira, Alexandru Tatomirescu, Ionut Tramandan, Roberto Scagnoli, Dan Istriteanu, Andrei-Edward Popa
The constant increase in the number of space objects and debris orbiting the Earth poses risks to satellites and other spacecraft, both in orbit and during the launching process. Therefore, the monitoring of space hazards to assess risk and prevent collisions has become part of the European Space Policy and requires the establishment of a dedicated Framework for Space Surveillance and Tracking (EU SST) Support. This article presents the CHEIA SST Radar, a new space tracking radar sensor developed and installed in Romania with the purpose of being included in the EU SST sensor network and of contributing to the joint database of space objects orbiting the Earth...
May 6, 2022: Sensors
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