Journal articles: '4QS'

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Mali, Mamta R., O. G. Bhusnure, Shrikrishna T. Mule, and S. S. Waghmare. "A Review on Life Cycle Management Approach on Asset Qualification." Journal of Drug Delivery and Therapeutics 10, no. 4 (July 15, 2020): 253–59. http://dx.doi.org/10.22270/jddt.v10i4.4146.

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All equipment’s used in the production of products shall be properly Validated, Qualified and Calibrated to demonstrate that it is suitable for its intended purpose. Qualification is an important aspect of the pharmaceutical quality system. When the equipment is properly qualified, verified and maintained, there is the possibility of Consistent performance of the equipment. A well designed qualification program saves valuable time and cost. Qualification is called a cyclic process because it is a never ending process. Appropriate documentation of the qualification program is very important as lack of the documented evidence does not give any meaning to qualification (Not documented it means not done). The current programs and procedures of equipment qualification used within any pharmaceutical and bioscience industry are based on ‘regulatory requirements’, ‘voluntary standards’, ‘vendor practices’, and ‘industry practices’. The output is considerable variation in the way any pharmaceutical and biotechnological companies approach for the laboratory equipment. The lifecycle management approach of equipment qualification covers entire life cycle for the specification, design, manufacturing, installation, commissioning, qualification (4Qs Model DQ, IQ, OQ, PQ), operation & maintenance of equipment in a risk based life cycle management approach. The goal of any regulated pharmaceutical and bioscience company is to provide reliable and valid data suitable for its intended purpose. Main goal of equipment qualification is to form the basis for written procedures for production and process control which are designed to assure that the drug products have the SISPQ (Safety, Identity, Strength, Purity and Quality) Keywords: Validation, Calibration, Life cycle management approach, Qualification (4Qs Model- DQ, IQ, OQ & PQ), SISPQ (Safety, Identity, Strength, Purity and Quality)

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Ghaffari, Meysam, Nasser Ghadiri, Mohammad Hossein Manshaei, and Mehran Sadeghi Lahijani. "$P^4QS$: A Peer-to-Peer Privacy Preserving Query Service for Location-Based Mobile Applications." IEEE Transactions on Vehicular Technology 66, no. 10 (October 2017): 9458–69. http://dx.doi.org/10.1109/tvt.2017.2703631.

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Herrmannová, Anna, Terezie Prilepskaja, Susan Wagner, Darina Šikrová, Jakub Zeman, Kristýna Poncová, and Leoš Shivaya Valášek. "Adapted formaldehyde gradient cross-linking protocol implicates human eIF3d and eIF3c, k and l subunits in the 43S and 48S pre-initiation complex assembly, respectively." Nucleic Acids Research 48, no. 4 (December 21, 2019): 1969–84. http://dx.doi.org/10.1093/nar/gkz1185.

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Abstract One of the key roles of the 12-subunit eukaryotic translation initiation factor 3 (eIF3) is to promote the formation of the 43S and 48S pre-initiation complexes (PICs). However, particular contributions of its individual subunits to these two critical initiation reactions remained obscure. Here, we adapted formaldehyde gradient cross-linking protocol to translation studies and investigated the efficiency of the 43S and 48S PIC assembly in knockdowns of individual subunits of human eIF3 known to produce various partial subcomplexes. We revealed that eIF3d constitutes an important intermolecular bridge between eIF3 and the 40S subunit as its elimination from the eIF3 holocomplex severely compromised the 43S PIC assembly. Similarly, subunits eIF3a, c and e were found to represent an important binding force driving eIF3 binding to the 40S subunit. In addition, we demonstrated that eIF3c, and eIF3k and l subunits alter the efficiency of mRNA recruitment to 43S PICs in an opposite manner. Whereas the eIF3c knockdown reduces it, downregulation of eIF3k or eIF3l increases mRNA recruitment, suggesting that the latter subunits possess a regulatory potential. Altogether this study provides new insights into the role of human eIF3 in the initial assembly steps of the translational machinery.

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Brito Querido, Jailson, Masaaki Sokabe, Sebastian Kraatz, Yuliya Gordiyenko, J. Mark Skehel, Christopher S. Fraser, and V. Ramakrishnan. "Structure of a human 48S translational initiation complex." Science 369, no. 6508 (September 3, 2020): 1220–27. http://dx.doi.org/10.1126/science.aba4904.

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A key step in translational initiation is the recruitment of the 43S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5′ end of messenger RNA (mRNA) to form the 48S initiation complex (i.e., the 48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo–electron microscopy to determine the structure of a reconstituted human 48S. The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43S. The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being “pulled” through the 40S subunit during scanning.

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Demydov, Оleksandr, Borys Liubarskyi, Valerii Domanskyi, Marina Glebova, Dmytro Iakunin, and Anna Tyshchenko. "Determination of optimal parameters of the pulse width modulation of the 4qs transducer for electriс rolling stock." Eastern-European Journal of Enterprise Technologies 5, no. 5 (95) (October 31, 2018): 29–38. http://dx.doi.org/10.15587/1729-4061.2018.143789.

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Abdelaziz, Hamdy. "Promoting Personalized Learning Design: The Role of Online Pedagogical Intervention." EDEN Conference Proceedings, no. 1 (June 16, 2019): 72–84. http://dx.doi.org/10.38069/edenconf-2019-ac-0010.

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Online learning technology and design has maximized and optimized the potential chances of personalized, customized, and adaptive learning. This theoretical paper is proposing a new dynamic pedagogical intervention model for effective personalized learning design. The author is trying to share a personal and practical answer to the following two questions: (a) What are the disruptive learning principles of the third renaissance learning paradigm that impact pedagogical engineering and intervention for personalized learning design? (b) What is the suggested model for effective online pedagogical intervention to promote personalized learning design? This perspective was guided by ten emergent disruptive learning principles of the third renaissance learning paradigm that impact online pedagogical engineering, management and intervention for personalized learning design. Effective online pedagogical intervention has four major dimensions that are grounded/interacted and focused on four metaphoric lenses: (a) types of learners (4Cs): Casual, Committed, Concentrated and Continuing; (b) pedagogical levels (4Ps): Intelligent, Agile, Distributed and Situated Pedagogy; (c) intervention levels (4Es): Enriching, Enhancing, Engaging and Empowering; and (d) online assessment frames (4As): Assessment of learning, Assessment for learning, Assessment as learning, and Assessment in learning.

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Glyzin, I. I., Yu M. Inkov, V. A. Kuchumov, and V. V. Litovchenko. "Improving the Energy Efficiency of a Traction Network and Electric Rolling Stock of Alternating Current with a 4qs-Converter." Russian Electrical Engineering 90, no. 9 (September 2019): 641–46. http://dx.doi.org/10.3103/s1068371219090050.

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Jivotovskaya, Antonina V., Leoš Valášek, Alan G. Hinnebusch, and Klaus H. Nielsen. "Eukaryotic Translation Initiation Factor 3 (eIF3) and eIF2 Can Promote mRNA Binding to 40S Subunits Independently of eIF4G in Yeast." Molecular and Cellular Biology 26, no. 4 (February 15, 2006): 1355–72. http://dx.doi.org/10.1128/mcb.26.4.1355-1372.2006.

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ABSTRACT Recruitment of the eukaryotic translation initiation factor 2 (eIF2)-GTP-Met-tRNAi Met ternary complex to the 40S ribosome is stimulated by multiple initiation factors in vitro, including eIF3, eIF1, eIF5, and eIF1A. Recruitment of mRNA is thought to require the functions of eIF4F and eIF3, with the latter serving as an adaptor between the ribosome and the 4G subunit of eIF4F. To define the factor requirements for these reactions in vivo, we examined the effects of depleting eIF2, eIF3, eIF5, or eIF4G in Saccharomyces cerevisiae cells on binding of the ternary complex, other initiation factors, and RPL41A mRNA to native 43S and 48S preinitiation complexes. Depleting eIF2, eIF3, or eIF5 reduced 40S binding of all constituents of the multifactor complex (MFC), comprised of these three factors and eIF1, supporting a mechanism of coupled 40S binding by MFC components. 40S-bound mRNA strongly accumulated in eIF5-depleted cells, even though MFC binding to 40S subunits was reduced by eIF5 depletion. Hence, stimulation of the GTPase activity of the ternary complex, a prerequisite for 60S subunit joining in vitro, is likely the rate-limiting function of eIF5 in vivo. Depleting eIF2 or eIF3 impaired mRNA binding to free 40S subunits, but depleting eIF4G led unexpectedly to accumulation of mRNA on 40S subunits. Thus, it appears that eIF3 and eIF2 are more critically required than eIF4G for stable binding of at least some mRNAs to native preinitiation complexes and that eIF4G has a rate-limiting function at a step downstream of 48S complex assembly in vivo.

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Pisareva, Vera P., and Andrey V. Pisarev. "DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context." Nucleic Acids Research 44, no. 9 (April 11, 2016): 4252–65. http://dx.doi.org/10.1093/nar/gkw240.

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Abstract During eukaryotic translation initiation, the 43S preinitiation complex (43S PIC), consisting of the 40S ribosomal subunit, eukaryotic initiation factors (eIFs) and initiator tRNA scans mRNA to find an appropriate start codon. Key roles in the accuracy of initiation codon selection belong to eIF1 and eIF1A, whereas the mammalian-specific DHX29 helicase substantially contributes to ribosomal scanning of structured mRNAs. Here, we show that DHX29 stimulates the recognition of the AUG codon but not the near-cognate CUG codon regardless of its nucleotide context during ribosomal scanning. The stimulatory effect depends on the contact between DHX29 and eIF1A. The unique DHX29 N-terminal domain binds to the ribosomal site near the mRNA entrance, where it contacts the eIF1A OB domain. UV crosslinking assays revealed that DHX29 may rearrange eIF1A and eIF2α in key nucleotide context positions of ribosomal complexes. Interestingly, DHX29 impedes the 48S initiation complex formation in the absence of eIF1A perhaps due to forming a physical barrier that prevents the 43S PIC from loading onto mRNA. Mutational analysis allowed us to split the mRNA unwinding and codon selection activities of DHX29. Thus, DHX29 is another example of an initiation factor contributing to start codon selection.

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YAMADA, Takayuki, Naoyuki TASHIRO, Yasuki TANAKA, and Tatsushi KOBAYASHI. "Research on the Applicability of “The Four Question Strategy (4QS)”to the Observations and Experiments in Science Textbooks of Elementary and Lower Secondary School." Journal of Research in Science Education 56, no. 1 (2015): 105–22. http://dx.doi.org/10.11639/sjst.sp14005.

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Kapoor, Devesh, Ruchi B. Vyas, and Diwaker Dadrwal. "AN OVERVIEW OF ANALYTICAL INSTRUMENT QUALIFICATION WITH REFERENCE OF PHARMACEUTICAL INDUSTRY." Journal of Drug Delivery and Therapeutics 8, no. 5 (September 6, 2018): 99–103. http://dx.doi.org/10.22270/jddt.v8i5.1858.

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In the most general sense, validation refers to a process that consists of at least four distinct components or steps: software, instruments, methods or procedures, and system suitability The system, the software, and the method must all be validated, and system suitability is used to keep the process in check. But while the overall process is called validation, some of the steps also are referred to by that same term, as well as other steps such as qualification and verification. Analytical instruments are used for a specific analysis. So regular performance verifications are made to ensure that the instrument to be used is suitable for its intended application. All equipments used in the production of products shall be properly Validated and Calibrated to demonstrate that it is suitable for its intended purpose. The current equipment qualification programs and procedures used within the pharmaceutical industry are based on regulatory requirements, voluntary standards, vendor practices, and industry practices. The result is considerable variation in the way pharmaceutical companies approach the qualification of laboratory equipment and the way they interpret the often vague requirements. The process for instrument qualification follows the 4Qs model approach. It include design qualification (DQ), Installation qualification (IQ), Operational qualification (OQ), Performance qualification (PQ). The goal of any regulated laboratory is to provide reliable and valid data suitable for its intended purpose. Analysts use validated methods, system suitability tests, and in-process quality control checks to ensure that the data they acquire are reliable and that there are specific guidance and procedures available to ensure compliance. Keywords: Qualification, FDA, Instruments, Validation, Calibration, Documentation

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Thakur, Anil, and Alan G. Hinnebusch. "eIF1 Loop 2 interactions with Met-tRNAi control the accuracy of start codon selection by the scanning preinitiation complex." Proceedings of the National Academy of Sciences 115, no. 18 (April 16, 2018): E4159—E4168. http://dx.doi.org/10.1073/pnas.1800938115.

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The eukaryotic 43S preinitiation complex (PIC), bearing initiator methionyl transfer RNA (Met-tRNAi) in a ternary complex (TC) with eukaryotic initiation factor 2 (eIF2)-GTP, scans the mRNA leader for an AUG codon in favorable context. AUG recognition evokes rearrangement from an open PIC conformation with TC in a “POUT” state to a closed conformation with TC more tightly bound in a “PIN” state. eIF1 binds to the 40S subunit and exerts a dual role of enhancing TC binding to the open PIC conformation while antagonizing the PIN state, necessitating eIF1 dissociation for start codon selection. Structures of reconstituted PICs reveal juxtaposition of eIF1 Loop 2 with the Met-tRNAi D loop in the PIN state and predict a distortion of Loop 2 from its conformation in the open complex to avoid a clash with Met-tRNAi. We show that Ala substitutions in Loop 2 increase initiation at both near-cognate UUG codons and AUG codons in poor context. Consistently, the D71A-M74A double substitution stabilizes TC binding to 48S PICs reconstituted with mRNA harboring a UUG start codon, without affecting eIF1 affinity for 40S subunits. Relatively stronger effects were conferred by arginine substitutions; and no Loop 2 substitutions perturbed the rate of TC loading on scanning 40S subunits in vivo. Thus, Loop 2–D loop interactions specifically impede Met-tRNAi accommodation in the PIN state without influencing the POUT mode of TC binding; and Arg substitutions convert the Loop 2–tRNAi clash to an electrostatic attraction that stabilizes PIN and enhances selection of poor start codons in vivo.

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Abu-Muriefah, Fadwa, and Amal Al-Rashed. "On the Diophantine Equation x2 = 4qn – 4qm + 9." Journal of King Abdulaziz University-Science 21, no. 1 (2009): 135–41. http://dx.doi.org/10.4197/sci.21-1.14.

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Wang, Yan. "Analysis on the Evolution and Innovation Essence of Product Life Cycle Oriented Marketing Theory." BCP Business & Management 17 (February 23, 2022): 28–34. http://dx.doi.org/10.54691/bcpbm.v17i.344.

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Every development of marketing theory is based on the gradual improvement of the previous theory and the summary of the practical test results. This paves the way for the emergence of renewal theory. According to the order of time, this paper takes 4Ps → NPs → 4Cs → 4Rs as the main line of discussion, and deeply expounds the principles and innovation development history of various marketing theories. And to carry on the substantive analysis research to them. Based on the product life cycle-oriented marketing theory evolution theory, this paper analyzes the essence and function of marketing from the current fierce business war. Then, starting from the four stages of product life cycle theory, this paper puts forward the marketing strategy of indifference applied in different stages of product life cycle and the problems that should be paid attention to in the process of enterprise marketing activities. The experimental data show that the proposed method can well describe the evolution process of marketing theory. This provides a certain reference value for the analysis of the essence of marketing innovation.

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Cuchalová, Lucie, Tomáš Kouba, Anna Herrmannová, István Dányi, Wen-ling Chiu, and Leoš Valášek. "The RNA Recognition Motif of Eukaryotic Translation Initiation Factor 3g (eIF3g) Is Required for Resumption of Scanning of Posttermination Ribosomes for Reinitiation on GCN4 and Together with eIF3i Stimulates Linear Scanning." Molecular and Cellular Biology 30, no. 19 (August 2, 2010): 4671–86. http://dx.doi.org/10.1128/mcb.00430-10.

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ABSTRACT Recent reports have begun unraveling the details of various roles of individual eukaryotic translation initiation factor 3 (eIF3) subunits in translation initiation. Here we describe functional characterization of two essential Saccharomyces cerevisiae eIF3 subunits, g/Tif35 and i/Tif34, previously suggested to be dispensable for formation of the 48S preinitiation complexes (PICs) in vitro. A triple-Ala substitution of conserved residues in the RRM of g/Tif35 (g/tif35-KLF) or a single-point mutation in the WD40 repeat 6 of i/Tif34 (i/tif34-Q258R) produces severe growth defects and decreases the rate of translation initiation in vivo without affecting the integrity of eIF3 and formation of the 43S PICs in vivo. Both mutations also diminish induction of GCN4 expression, which occurs upon starvation via reinitiation. Whereas g/tif35-KLF impedes resumption of scanning for downstream reinitiation by 40S ribosomes terminating at upstream open reading frame 1 (uORF1) in the GCN4 mRNA leader, i/tif34-Q258R prevents full GCN4 derepression by impairing the rate of scanning of posttermination 40S ribosomes moving downstream from uORF1. In addition, g/tif35-KLF reduces processivity of scanning through stable secondary structures, and g/Tif35 specifically interacts with Rps3 and Rps20 located near the ribosomal mRNA entry channel. Together these results implicate g/Tif35 and i/Tif34 in stimulation of linear scanning and, specifically in the case of g/Tif35, also in proper regulation of the GCN4 reinitiation mechanism.

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Foiani, M., A. M. Cigan, C. J. Paddon, S. Harashima, and A. G. Hinnebusch. "GCD2, a translational repressor of the GCN4 gene, has a general function in the initiation of protein synthesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 6 (June 1991): 3203–16. http://dx.doi.org/10.1128/mcb.11.6.3203.

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The GCD2 protein is a translational repressor of GCN4, the transcriptional activator of multiple amino acid biosynthetic genes in Saccharomyces cerevisiae. We present evidence that GCD2 has a general function in the initiation of protein synthesis in addition to its gene-specific role in translational control of GCN4 expression. Two temperature-sensitive lethal gcd2 mutations result in sensitivity to inhibitors of protein synthesis at the permissive temperature, and the gcd2-503 mutation leads to reduced incorporation of labeled leucine into total protein following a shift to the restrictive temperature of 36 degrees C. The gcd2-503 mutation also results in polysome runoff, accumulation of inactive 80S ribosomal couples, and accumulation of at least one of the subunits of the general translation initiation factor 2 (eIF-2 alpha) in 43S-48S particles following a shift to the restrictive temperature. The gcd2-502 mutation causes accumulation of 40S subunits in polysomes, known as halfmers, that are indicative of reduced 40S-60S subunit joining at the initiation codon. These phenotypes suggest that GCD2 functions in the translation initiation pathway at a step following the binding of eIF-2.GTP.Met-tRNA(iMet) to 40S ribosomal subunits. consistent with this hypothesis, we found that inhibiting 40S-60S subunit joining by deleting one copy (RPL16B) of the duplicated gene encoding the 60S ribosomal protein L16 qualitatively mimics the phenotype of gcd2 mutations in causing derepression of GCN4 expression under nonstarvation conditions. However, deletion of RPL16B also prevents efficient derepression of GCN4 under starvation conditions, indicating that lowering the concentration of 60S subunits and reducing GCD2 function affect translation initiation at GCN4 in different ways. This distinction is in accord with a recently proposed model for GCN4 translational control in which ribosomal reinitiation at short upstream open reading frames in the leader of GCN4 mRNA is suppressed under amino acid starvation conditions to allow for increased reinitiation at the GCN4 start codon.

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Foiani, M., A. M. Cigan, C. J. Paddon, S. Harashima, and A. G. Hinnebusch. "GCD2, a translational repressor of the GCN4 gene, has a general function in the initiation of protein synthesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 6 (June 1991): 3203–16. http://dx.doi.org/10.1128/mcb.11.6.3203-3216.1991.

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The GCD2 protein is a translational repressor of GCN4, the transcriptional activator of multiple amino acid biosynthetic genes in Saccharomyces cerevisiae. We present evidence that GCD2 has a general function in the initiation of protein synthesis in addition to its gene-specific role in translational control of GCN4 expression. Two temperature-sensitive lethal gcd2 mutations result in sensitivity to inhibitors of protein synthesis at the permissive temperature, and the gcd2-503 mutation leads to reduced incorporation of labeled leucine into total protein following a shift to the restrictive temperature of 36 degrees C. The gcd2-503 mutation also results in polysome runoff, accumulation of inactive 80S ribosomal couples, and accumulation of at least one of the subunits of the general translation initiation factor 2 (eIF-2 alpha) in 43S-48S particles following a shift to the restrictive temperature. The gcd2-502 mutation causes accumulation of 40S subunits in polysomes, known as halfmers, that are indicative of reduced 40S-60S subunit joining at the initiation codon. These phenotypes suggest that GCD2 functions in the translation initiation pathway at a step following the binding of eIF-2.GTP.Met-tRNA(iMet) to 40S ribosomal subunits. consistent with this hypothesis, we found that inhibiting 40S-60S subunit joining by deleting one copy (RPL16B) of the duplicated gene encoding the 60S ribosomal protein L16 qualitatively mimics the phenotype of gcd2 mutations in causing derepression of GCN4 expression under nonstarvation conditions. However, deletion of RPL16B also prevents efficient derepression of GCN4 under starvation conditions, indicating that lowering the concentration of 60S subunits and reducing GCD2 function affect translation initiation at GCN4 in different ways. This distinction is in accord with a recently proposed model for GCN4 translational control in which ribosomal reinitiation at short upstream open reading frames in the leader of GCN4 mRNA is suppressed under amino acid starvation conditions to allow for increased reinitiation at the GCN4 start codon.

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Kolupaeva, Victoria G., Tatyana V. Pestova, and Christopher U. T. Hellen. "An Enzymatic Footprinting Analysis of the Interaction of 40S Ribosomal Subunits with the Internal Ribosomal Entry Site of Hepatitis C Virus." Journal of Virology 74, no. 14 (July 15, 2000): 6242–50. http://dx.doi.org/10.1128/jvi.74.14.6242-6250.2000.

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ABSTRACT Hepatitis C virus translation is initiated on a ∼330-nucleotide (nt)-long internal ribosomal entry site (IRES) at the 5′ end of the genome. In this process, a 43S preinitiation complex (comprising a 40S ribosomal subunit, eukaryotic initiation factor 3 (eIF3), and a ternary [eIF2-GTP-initiator tRNA] complex) binds the IRES in a precise manner so that the initiation codon is placed at the ribosomal P site. This binding step involves specific interactions between the IRES and different components of the 43S complex. The 40S subunit and eIF3 can bind to the IRES independently; previous analyses revealed that eIF3 binds specifically to an apical half of IRES domain III. Nucleotides in the IRES that are involved in the interaction with the 40S subunit were identified by RNase footprinting and mapped to the basal half of domain III and in domain IV. Interaction sites were identified in locations that have been found to be essential for IRES function, including (i) the apical loop residues GGG266-268 in subdomain IIId and (ii) the pseudoknot. Extensive protection from RNase cleavage also occurred downstream of the pseudoknot in domain IV, flanking both sides of the initiation codon and corresponding in length to that of the mRNA-binding cleft of the 40S subunit. These results indicate that the 40S subunit makes multiple interactions with the IRES and suggest that only nucleotides in domain IV are inserted into the mRNA-binding cleft of the 40S subunit.

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Dong, Jinsheng, Colin Echeverría Aitken, Anil Thakur, Byung-Sik Shin, Jon R. Lorsch, and Alan G. Hinnebusch. "Rps3/uS3 promotes mRNA binding at the 40S ribosome entry channel and stabilizes preinitiation complexes at start codons." Proceedings of the National Academy of Sciences 114, no. 11 (February 21, 2017): E2126—E2135. http://dx.doi.org/10.1073/pnas.1620569114.

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The eukaryotic 43S preinitiation complex (PIC) bearing Met-tRNAiMet in a ternary complex (TC) with eukaryotic initiation factor (eIF)2-GTP scans the mRNA leader for an AUG codon in favorable “Kozak” context. AUG recognition provokes rearrangement from an open PIC conformation with TC bound in a state not fully engaged with the P site (“POUT”) to a closed, arrested conformation with TC tightly bound in the “PIN” state. Yeast ribosomal protein Rps3/uS3 resides in the mRNA entry channel of the 40S subunit and contacts mRNA via conserved residues whose functional importance was unknown. We show that substitutions of these residues reduce bulk translation initiation and diminish initiation at near-cognate UUG start codons in yeast mutants in which UUG selection is abnormally high. Two such substitutions—R116D and R117D—also increase discrimination against an AUG codon in suboptimal Kozak context. Consistently, the Arg116 and Arg117 substitutions destabilize TC binding to 48S PICs reconstituted in vitro with mRNA harboring a UUG start codon, indicating destabilization of the closed PIN state with a UUG–anticodon mismatch. Using model mRNAs lacking contacts with either the mRNA entry or exit channels of the 40S subunit, we demonstrate that Arg116/Arg117 are crucial for stabilizing PIC–mRNA contacts at the entry channel, augmenting the function of eIF3 at both entry and exit channels. The corresponding residues in bacterial uS3 promote the helicase activity of the elongating ribosome, suggesting that uS3 contacts with mRNA enhance multiple phases of translation across different domains of life.

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Jones, Nicola, Craig Lammas, and Carl Gwinnutt. "Poor recall of “4Hs and 4Ts” by medical staff." Resuscitation 81, no. 11 (November 2010): 1600. http://dx.doi.org/10.1016/j.resuscitation.2010.06.015.

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Sokabe, Masaaki, and Christopher S. Fraser. "A helicase-independent activity of eIF4A in promoting mRNA recruitment to the human ribosome." Proceedings of the National Academy of Sciences 114, no. 24 (May 30, 2017): 6304–9. http://dx.doi.org/10.1073/pnas.1620426114.

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In the scanning model of translation initiation, the decoding site and latch of the 40S subunit must open to allow the recruitment and migration of messenger RNA (mRNA); however, the precise molecular details for how initiation factors regulate mRNA accommodation into the decoding site have not yet been elucidated. Eukaryotic initiation factor (eIF) 3j is a subunit of eIF3 that binds to the mRNA entry channel and A-site of the 40S subunit. Previous studies have shown that a reduced affinity of eIF3j for the 43S preinitiation complex (PIC) occurs on eIF4F-dependent mRNA recruitment. Because eIF3j and mRNA bind anticooperatively to the 43S PIC, reduced eIF3j affinity likely reflects a state of full accommodation of mRNA into the decoding site. Here, we have used a fluorescence-based anisotropy assay to quantitatively determine how initiation components coordinate their activities to reduce the affinity of eIF3j during the recruitment of mRNA to the 43S PIC. Unexpectedly, we show that a full reduction in eIF3j affinity for the 43S PIC requires an ATP-dependent, but unwinding-independent, activity of eIF4A. This result suggests that in addition to its helicase activity, eIF4A uses the free energy of ATP binding and hydrolysis as a regulatory switch to control the conformation of the 43S PIC during mRNA recruitment. Therefore, our results define eIF4A as a universal initiation factor in cap-dependent translation initiation that functions beyond its role in RNA unwinding.

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Dundr, Miroslav, and Mark O. J. Olson. "Partially Processed pre-rRNA Is Preserved in Association with Processing Components in Nucleolus-derived Foci during Mitosis." Molecular Biology of the Cell 9, no. 9 (September 1998): 2407–22. http://dx.doi.org/10.1091/mbc.9.9.2407.

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Previous studies showed that components implicated in pre-rRNA processing, including U3 small nucleolar (sno)RNA, fibrillarin, nucleolin, and proteins B23 and p52, accumulate in perichromosomal regions and in numerous mitotic cytoplasmic particles, termed nucleolus-derived foci (NDF) between early anaphase and late telophase. The latter structures were analyzed for the presence of pre-rRNA by fluorescence in situ hybridization using probes for segments of pre-rRNA with known half-lives. The NDF did not contain the short-lived 5′-external transcribed spacer (ETS) leader segment upstream from the primary processing site in 47S pre-rRNA. However, the NDF contained sequences from the 5′-ETS core, 18S, internal transcribed spacer 1 (ITS1), and 28S segments and also had detectable, but significantly reduced, levels of the 3′-ETS sequence. Northern analyses showed that in mitotic cells, the latter sequences were present predominantly in 45S-46S pre-rRNAs, indicating that high-molecular weight processing intermediates are preserved during mitosis. Two additional essential processing components were also found in the NDF: U8 snoRNA and hPop1 (a protein component of RNase MRP and RNase P). Thus, the NDF appear to be large complexes containing partially processed pre-rRNA associated with processing components in which processing has been significantly suppressed. The NDF may facilitate coordinated assembly of postmitotic nucleoli.

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Xu, Kaijie, Xinyao He, Susanne Dreisigacker, Zhonghu He, and Pawan K. Singh. "Anther Extrusion and Its Association with Fusarium Head Blight in CIMMYT Wheat Germplasm." Agronomy 10, no. 1 (December 28, 2019): 47. http://dx.doi.org/10.3390/agronomy10010047.

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Pronounced anther extrusion (AE) is associated with field resistance to Fusarium head blight (FHB), one of the most devastating diseases of wheat globally. In this study, two recombinant inbred line (RIL) populations were used to map quantitative trait loci (QTL) for AE and field FHB resistance and to investigate the association of both traits at the genetic level. Furthermore, two panels of International Maize and Wheat Improvement Center (CIMMYT) wheat breeding lines were evaluated to describe the phenotypic association between the two traits in detail. Highly significant negative correlation was identified between AE and FHB severity in the two populations and the two panels, with r-values ranging from 0.55 to 0.74. QTL analysis in the two RIL populations identified 12 QTL for AE and nine for FHB resistance, of which five QTL located on chromosomes 3BL, 4BS, 4DS, 5AL, and 5BL were associated with both AE and FHB, collectively explaining over 50% of phenotypic variation for FHB. The QTL on chromosomes 4BS, 4DS, 5AL, and 5BL were closely linked to Rht-B1, Rht-D1, Vrn-A1, and Vrn-B1 genes, respectively. In conclusion, AE is closely related to field FHB resistance and could be used as a morphological marker in wheat breeding for field FHB resistance.

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Festa, Giuseppe, Maria Teresa Cuomo, Gerardino Metallo, and Antonio Festa. "The (r)evolution of wine marketing mix: From the 4Ps to the 4Es." Journal of Business Research 69, no. 5 (May 2016): 1550–55. http://dx.doi.org/10.1016/j.jbusres.2015.10.015.

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Barnett, S. F., T. A. Theiry, and W. M. LeStourgeon. "The core proteins A2 and B1 exist as (A2)3B1 tetramers in 40S nuclear ribonucleoprotein particles." Molecular and Cellular Biology 11, no. 2 (February 1991): 864–71. http://dx.doi.org/10.1128/mcb.11.2.864.

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The six "core" proteins of HeLa cell 40S nuclear ribonucleoprotein particles (hnRNP particles) package 700-nucleotide lengths of pre-mRNA into a repeating array of regular particles. We have previously shown that the C proteins exist as anisotropic tetramers of (C1)3C2 in 40S hnRNP particles and that each particle probably contains three such tetramers. We report here that proteins A2 and B1 also exist in monoparticles as (A2)3B1 tetramers and that each monoparticle contains at least three such tetramers. Proteins A2 and B1 dissociate from isolated monoparticles as a stable tetramer upon nuclease digestion. In low-salt gradients, the tetramers sediment at 6.8S, which is consistent with a mass of 145 kDa. In 200 mM salt, the concentration which dissociates these proteins from RNA, only 4.2S dimers exist in solution. Tetramers of (A2)3B1 possess the ability to package multiples of 700 nucleotides of RNA in vitro into an array of regular, 22.5-nm 43S particles. Unlike the in vitro assembly of intact 40S hnRNP, the (A2)3B1 tetramers assemble by means of a highly cooperative process. These findings indicate that the (A2)3B1 tetramers play a major role in hnRNP assembly and they further support the contention that 40S monoparticles are regular structures composed of three copies of three different tetramers, i.e., 3[(A1)3B2, (A2)3B1, (C1)3C2].

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Barnett, S. F., T. A. Theiry, and W. M. LeStourgeon. "The core proteins A2 and B1 exist as (A2)3B1 tetramers in 40S nuclear ribonucleoprotein particles." Molecular and Cellular Biology 11, no. 2 (February 1991): 864–71. http://dx.doi.org/10.1128/mcb.11.2.864-871.1991.

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The six "core" proteins of HeLa cell 40S nuclear ribonucleoprotein particles (hnRNP particles) package 700-nucleotide lengths of pre-mRNA into a repeating array of regular particles. We have previously shown that the C proteins exist as anisotropic tetramers of (C1)3C2 in 40S hnRNP particles and that each particle probably contains three such tetramers. We report here that proteins A2 and B1 also exist in monoparticles as (A2)3B1 tetramers and that each monoparticle contains at least three such tetramers. Proteins A2 and B1 dissociate from isolated monoparticles as a stable tetramer upon nuclease digestion. In low-salt gradients, the tetramers sediment at 6.8S, which is consistent with a mass of 145 kDa. In 200 mM salt, the concentration which dissociates these proteins from RNA, only 4.2S dimers exist in solution. Tetramers of (A2)3B1 possess the ability to package multiples of 700 nucleotides of RNA in vitro into an array of regular, 22.5-nm 43S particles. Unlike the in vitro assembly of intact 40S hnRNP, the (A2)3B1 tetramers assemble by means of a highly cooperative process. These findings indicate that the (A2)3B1 tetramers play a major role in hnRNP assembly and they further support the contention that 40S monoparticles are regular structures composed of three copies of three different tetramers, i.e., 3[(A1)3B2, (A2)3B1, (C1)3C2].

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Kimball, Scot R., Rick L. Horetsky, David Ron, Leonard S. Jefferson, and Heather P. Harding. "Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes." American Journal of Physiology-Cell Physiology 284, no. 2 (February 1, 2003): C273—C284. http://dx.doi.org/10.1152/ajpcell.00314.2002.

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In eukaryotic cells subjected to environmental stress, untranslated mRNA accumulates in discrete cytoplasmic foci that have been termed stress granules. Recent studies have shown that in addition to mRNA, stress granules also contain 40S ribosomal subunits and various translation initiation factors, including the mRNA binding proteins eIF4E and eIF4G. However, eIF2, the protein that transfers initiator methionyl-tRNAi(Met-tRNAi) to the 40S ribosomal subunit, has not been detected in stress granules. This result is surprising because the eIF2 · GTP · Met-tRNAi complex is thought to bind to the 40S ribosomal subunit before the eIF4G · eIF4E · mRNA complex. In the present study, we show in both NIH-3T3 cells and mouse embryo fibroblasts that stress granules contain not only eIF2 but also the guanine nucleotide exchange factor for eIF2, eIF2B. Moreover, we show that phosphorylation of the α-subunit of eIF2 is necessary and sufficient for stress granule formation during the unfolded protein response. Finally, we also show that stress granules contain many, if not all, of the components of the 48S preinitiation complex, but not 60S ribosomal subunits, suggesting that they represent stalled translation initiation complexes.

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Pisarev, Andrey V., Louisa S. Chard, Yoshihiro Kaku, Helen L. Johns, Ivan N. Shatsky, and Graham J. Belsham. "Functional and Structural Similarities between the Internal Ribosome Entry Sites of Hepatitis C Virus and Porcine Teschovirus, a Picornavirus." Journal of Virology 78, no. 9 (May 1, 2004): 4487–97. http://dx.doi.org/10.1128/jvi.78.9.4487-4497.2004.

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ABSTRACT Initiation of protein synthesis on picornavirus RNA requires an internal ribosome entry site (IRES). Typically, picornavirus IRES elements contain about 450 nucleotides (nt) and use most of the cellular translation initiation factors. However, it is now shown that just 280 nt of the porcine teschovirus type 1 Talfan (PTV-1) 5′ untranslated region direct the efficient internal initiation of translation in vitro and within cells. In toeprinting assays, assembly of 48S preinitiation complexes from purified components on the PTV-1 IRES was achieved with just 40S ribosomal subunits plus eIF2 and Met-tRNAi Met. Indeed, a binary complex between 40S subunits and the PTV-1 IRES is formed. Thus, the PTV-1 IRES has properties that are entirely different from other picornavirus IRES elements but highly reminiscent of the hepatitis C virus (HCV) IRES. Comparison between the PTV-1 IRES and HCV IRES elements revealed islands of high sequence identity that occur in regions critical for the interactions of the HCV IRES with the 40S ribosomal subunit and eIF3. Thus, there is significant functional and structural similarity between the IRES elements from the picornavirus PTV-1 and HCV, a flavivirus.

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Ryabova, L., H. S. Park, and T. Hohn. "Control of translation reinitiation on the cauliflower mosaic virus (CaMV) polycistronic RNA." Biochemical Society Transactions 32, no. 4 (August 1, 2004): 592–96. http://dx.doi.org/10.1042/bst0320592.

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Translation of the polycistronic 35S RNA of CaMV (cauliflower mosaic virus) occurs via a reinitiation mechanism, which requires TAV (transactivator/viroplasmin). To allow translation reinitiation of the major open reading frames on the polycistronic RNA, TAV interacts with the host translational machinery via eIF3 (eukaryotic initiation factor 3) and the 60S ribosome. Accumulation of TAV and eIF3 in the polysomal fraction isolated from CaMV-infected cells suggested that TAV prevents loss of eIF3 from the translating ribosomes during the first initiation event. The TAV–eIF3–80S complex could be detected in vitro by sucrose-gradient-sedimentation analysis. The question is whether TAV interacts directly with the 48S preinitiation complex or enters polysomes after the first initiation event. eIF4B, a component of the 48S initiation complex, can preclude formation of the TAV–eIF3 complex via competition with TAV for eIF3 binding; the eIF4B- and TAV-binding sites on eIF3g overlap. eIF4B out-competes TAV for binding to eIF3 and to the eIF3–40S complex. Transient overexpression of eIF4B in plant protoplasts specifically inhibits TAV-mediated transactivation of polycistronic translation. Our results thus indicate that eIF4B precludes TAV–eIF3–40S complex formation during the first initiation event. Consequently, overexpression of TAV in plant protoplasts affects only the second and subsequent initiation events. We propose a model in which TAV enters the host translational machinery at the eIF4B-removal step to stabilize eIF3 within polysomes.

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Ramirez, M., R. C. Wek, and A. G. Hinnebusch. "Ribosome association of GCN2 protein kinase, a translational activator of the GCN4 gene of Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 6 (June 1991): 3027–36. http://dx.doi.org/10.1128/mcb.11.6.3027.

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The GCN4 gene of the yeast Saccharomyces cerevisiae encodes a transcriptional activator of amino acid biosynthetic genes that is regulated at the translational level according to the availability of amino acids. GCN2 is a protein kinase required for increased translation of GCN4 mRNA in amino acid-starved cells. Centrifugation of cell extracts in sucrose gradients indicated that GCN2 comigrates with ribosomal subunits and polysomes. The fraction of GCN2 cosedimenting with polysomes was reduced under conditions in which polysomes were dissociated, suggesting that GCN2 is physically bound to these structures. When the association of 40S and 60S subunits was prevented by omitting Mg2+ from the gradient, almost all of the GCN2 comigrated with 60S ribosomal subunits, and it remained bound to these particles during gel electrophoresis under nondenaturing conditions. GCN2 could be dissociated from 60S subunits by 0.5 M KCl, suggesting that it is loosely associated with ribosomes rather than being an integral ribosomal protein. Accumulation of GCN2 on free 43S-48S particles and 60S subunits occurred during polysome runoff in vitro and under conditions of reduced growth rate in vivo. These observations, plus the fact that GCN2 shows preferential association with free ribosomal subunits during exponential growth, suggest that GCN2 interacts with ribosomes during the translation initiation cycle. The extreme carboxyl-terminal segment of GCN2 is essential for its interaction with ribosomes. These sequences are also required for the ability of GCN2 to stimulate GCN4 translation in vivo, leading us to propose that ribosome association by GCN2 is important for its access to substrates in the translational machinery or for detecting uncharged tRNA in amino acid-starved cells.

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Ramirez, M., R. C. Wek, and A. G. Hinnebusch. "Ribosome association of GCN2 protein kinase, a translational activator of the GCN4 gene of Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 6 (June 1991): 3027–36. http://dx.doi.org/10.1128/mcb.11.6.3027-3036.1991.

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The GCN4 gene of the yeast Saccharomyces cerevisiae encodes a transcriptional activator of amino acid biosynthetic genes that is regulated at the translational level according to the availability of amino acids. GCN2 is a protein kinase required for increased translation of GCN4 mRNA in amino acid-starved cells. Centrifugation of cell extracts in sucrose gradients indicated that GCN2 comigrates with ribosomal subunits and polysomes. The fraction of GCN2 cosedimenting with polysomes was reduced under conditions in which polysomes were dissociated, suggesting that GCN2 is physically bound to these structures. When the association of 40S and 60S subunits was prevented by omitting Mg2+ from the gradient, almost all of the GCN2 comigrated with 60S ribosomal subunits, and it remained bound to these particles during gel electrophoresis under nondenaturing conditions. GCN2 could be dissociated from 60S subunits by 0.5 M KCl, suggesting that it is loosely associated with ribosomes rather than being an integral ribosomal protein. Accumulation of GCN2 on free 43S-48S particles and 60S subunits occurred during polysome runoff in vitro and under conditions of reduced growth rate in vivo. These observations, plus the fact that GCN2 shows preferential association with free ribosomal subunits during exponential growth, suggest that GCN2 interacts with ribosomes during the translation initiation cycle. The extreme carboxyl-terminal segment of GCN2 is essential for its interaction with ribosomes. These sequences are also required for the ability of GCN2 to stimulate GCN4 translation in vivo, leading us to propose that ribosome association by GCN2 is important for its access to substrates in the translational machinery or for detecting uncharged tRNA in amino acid-starved cells.

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Corell, R. A., L. K. Read, G. R. Riley, J. K. Nellissery, T. E. Allen, M. L. Kable, M. D. Wachal, S. D. Seiwert, P. J. Myler, and K. D. Stuart. "Complexes from Trypanosoma brucei that exhibit deletion editing and other editing-associated properties." Molecular and Cellular Biology 16, no. 4 (April 1996): 1410–18. http://dx.doi.org/10.1128/mcb.16.4.1410.

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Transcripts from many mitochondrial genes in kinetoplastids undergo RNA editing, a posttranscriptional process which inserts and deletes uridines. By assaying for deletion editing in vitro, we found that the editing activity from Trypanosoma brucei mitochondrial lysates (S.D. Seiwert and K.D. Stuart), Science 266:114-117,1994) sediments with a peak of approximately 20S. RNA helicase, terminal uridylyl transferase, RNA ligase, and adenylation activities, which may have a role in editing, cosediment in a broad distribution, with most of each activity at 35 to 40S. Most ATPase 6 (A6) guide RNA and unedited A6 mRNA sediments at 20 to 30S, with some sedimenting further into the gradient, while most edited A6 mRNA sediments at >35S. Several mitochondrial proteins which cross-link specifically with guide RNA upon UV treatment also sediment in glycerol gradients. Notably, a 65-kDa protein sediments primarily at approximately 20S, a 90-kDa protein sediments at 35 to 40S, and a 25-kDa protein is present at <10S. Most ribonucleoprotein complexes that form with gRNA in vitro sediment at 10 to 20S, except for one, which sediments at 30 to 45S. These results suggest that RNA editing takes place within a multicomponent complex. The potential functions of and relationships between the 20S and 35 to 40S complexes are discussed.

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KANEKO, Kenji, and Tatsushi KOBAYASHI. "Study of Effects on Graph-making Capability of Teaching the Building up of a Hypothesis Based on the Four-question Strategy (4QS), Using a Course of Study for Junior High Schools : "the Magnitude of Force and the Elongation of Springs", as an Example." Journal of Research in Science Education 51, no. 3 (March 10, 2011): 75–83. http://dx.doi.org/10.11639/sjst.kj00007111463.

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Sweeney, Trevor R., Vidya Dhote, Ewelina Guca, Christopher U. T. Hellen, Yaser Hashem, and Tatyana V. Pestova. "Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs." Nucleic Acids Research 49, no. 22 (December 9, 2021): 12955–69. http://dx.doi.org/10.1093/nar/gkab1192.

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Abstract Translation initiation on structured mammalian mRNAs requires DHX29, a DExH protein that comprises a unique 534-aa-long N-terminal region (NTR) and a common catalytic DExH core. DHX29 binds to 40S subunits and possesses 40S-stimulated NTPase activity essential for its function. In the cryo-EM structure of DHX29-bound 43S preinitiation complexes, the main DHX29 density resides around the tip of helix 16 of 18S rRNA, from which it extends through a linker to the subunit interface forming an intersubunit domain next to the eIF1A binding site. Although a DExH core model can be fitted to the main density, the correlation between the remaining density and the NTR is unknown. Here, we present a model of 40S-bound DHX29, supported by directed hydroxyl radical cleavage data, showing that the intersubunit domain comprises a dsRNA-binding domain (dsRBD, aa 377–448) whereas linker corresponds to the long α-helix (aa 460–512) that follows the dsRBD. We also demonstrate that the N-terminal α-helix and the following UBA-like domain form a four-helix bundle (aa 90–166) that constitutes a previously unassigned section of the main density and resides between DHX29’s C-terminal α-helix and the linker. In vitro reconstitution experiments revealed the critical and specific roles of these NTR elements for DHX29’s function.

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Xu, Guang Ying. "The Transient Temperature and Thermal Stresses on Metal Material Irradiated by Multi-Pulse Short Power." Applied Mechanics and Materials 130-134 (October 2011): 873–78. http://dx.doi.org/10.4028/www.scientific.net/amm.130-134.873.

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Based on the non-Fourier law and thermo-elastic theory, the non-Fourier expressions of the temperature field and the thermal stress field of metal material under multi-pulse laser irradiation were deduced. Taken stainless metal and two pulse width (ω=4ps,4fs) as an example, The effects that distributions and variations of transient temperature and thermal stress are influenced by laser pulse width are studied. The results show that the magnitude and frequency of transient temperature and thermal stress are seriously affected by the laser pulse width. More narrower the laser pulse width, faster and higher the local temperature rise; as well as the thermal stresses.

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Dmitriev, Sergei E., Ilya M. Terenin, Yan E. Dunaevsky, William C. Merrick, and Ivan N. Shatsky. "Assembly of 48S Translation Initiation Complexesfrom Purified Components with mRNAs That Have Some Base Pairingwithin Their 5′ UntranslatedRegions." Molecular and Cellular Biology 23, no. 24 (December 15, 2003): 8925–33. http://dx.doi.org/10.1128/mcb.23.24.8925-8933.2003.

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ABSTRACT The reconstitution of translation initiation complexes from purified components is a reliable approach to determine the complete set of essential canonical initiation factors and auxiliary proteins required for the 40S ribosomal subunit to locate the initiation codon on individual mRNAs. Until now, it has been successful mostly for formation of 48S translation initiation complexes with viral IRES elements. Among cap-dependent mRNAs, only globin mRNAs and transcripts with artificial 5′ leaders were amenable to this assembly. Here, with modified conditions for the reconstitution, 48S complexes have been successfully assembled with the 5′ UTR of beta-actin mRNA (84 nucleotides) and the tripartite leader of adenovirus RNAs (232 nucleotides), though the latter has been able to use only the scanning rather then the shunting model of translation initiation with canonical initiation factors. We show that initiation factor 4B is essential for mRNAs that have even a rather moderate base pairing within their 5′ UTRs (with the cumulative stability of the secondary structure within the entire 5′ UTR < −13 kcal/mol) and not essential for beta-globin mRNA. A recombinant eIF4B poorly substitutes for the native factor. The 5′ UTRs with base-paired G residues reveal a very sharp dependence on the eIF4B concentration to form the 48S complex. The data suggest that even small variations in concentration or activity of eIF4B in mammalian cells may differentially affect the translation of different classes of cap-dependent cellular mRNAs.

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Dai, Yi, Pidong Li, Zhiqiang Wang, Fan Liang, Fan Yang, Li Fang, Yu Huang, et al. "Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)." Journal of Medical Genetics 57, no. 2 (September 10, 2019): 109–20. http://dx.doi.org/10.1136/jmedgenet-2019-106078.

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PurposeFacioscapulohumeral muscular dystrophy (FSHD) is a common adult muscular dystrophy. Over 95% of FSHD cases are associated with contraction of the D4Z4 tandem repeat (~3.3 kb per unit) at 4q35 with a specific genomic configuration (haplotype) called 4qA. Molecular diagnosis of FSHD typically requires pulsed-field gel electrophoresis with Southern blotting. We aim to develop novel genomic and computational methods for characterising D4Z4 repeat numbers in FSHD.MethodsWe leveraged a single-molecule optical mapping platform that maps locations of restriction enzyme sites on high molecular weight (>150 kb) DNA molecules. We developed bioinformatics methods to address several challenges, including the differentiation of 4qA with 4qB alleles, the differentiation of 4q35 and 10q26 segmental duplications, the quantification of repeat numbers with different enzymes that may or may not have recognition sites within D4Z4 repeats. We evaluated the method on 25 human subjects (13 patients, 3 individual control subjects, 9 control subjects from 3 families) labelled by the Nb.BssSI and/or Nt.BspQI enzymes.ResultsWe demonstrated that the method gave a direct quantitative measurement of repeat numbers on D4Z4 repeats with 4qA allelic configuration and the levels of postzygotic mosaicism. Our method had high concordance with Southern blots from several cohorts on two platforms (Bionano Saphyr and Bionano Irys), but with improved quantification of repeat numbers.ConclusionWhile the study is limited by small sample size, our results demonstrated that single-molecule optical mapping is a viable approach for more refined analysis on genotype-phenotype relationships in FSHD, especially when postzygotic mosaicism is present.

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Stec, Michael J., David L. Mayhew, and Marcas M. Bamman. "The effects of age and resistance loading on skeletal muscle ribosome biogenesis." Journal of Applied Physiology 119, no. 8 (October 15, 2015): 851–57. http://dx.doi.org/10.1152/japplphysiol.00489.2015.

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The hypertrophic response to resistance training is generally attenuated with aging; yet the mechanisms regulating this phenomenon are largely unknown. Several studies to date have shown blunted translational efficiency following acute resistance exercise in older adults; however, the effects on translational capacity (i.e., ribosome biogenesis) have not yet been examined. Thus the purpose of this study was to examine changes in markers of ribosome biogenesis following an acute bout of resistance loading (RL; 9 sets × 10 repetitions of knee extensions) in younger (Y; n = 14; 39.2 ± 4.1 yr) and older (O; n = 12; 75.7 ± 5.7 yr) adults. Vastus lateralis biopsies were taken pre- and 24 h post-RL, and muscle samples were analyzed for total RNA content, 45S pre-rRNA expression, ribosomal protein content, and levels of signaling proteins that regulate ribosome biogenesis. Before RL, O had higher total RNA content (+28%; P < 0.05), a trend toward higher 45S pre-rRNA expression (+59%; P = 0.08), and greater protein content of several ribosomal components (≈ +50–80%; P < 0.05) than Y. However, 24 h post-RL, only Y increased 45S pre-rRNA expression (+34%; P < 0.01), possibly driven by higher basal p-Rb (Ser780) (+61%; P = 0.10), and a robust transcription initiation factor (TIF)-1a response (+75%; P < 0.05). RL tended to increase protein components of the 40S ribosomal subunit in Y only (≈ +20–25%; P ≤ 0.12). Overall, the data suggest blunted ribosome biogenesis in response to RL in O, which may be a potential mechanism driving the age-related attenuation of resistance training-induced hypertrophy.

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Lothstein, L., H. P. Arenstorf, S. Y. Chung, B. W. Walker, J. C. Wooley, and W. M. LeStourgeon. "General organization of protein in HeLa 40S nuclear ribonucleoprotein particles." Journal of Cell Biology 100, no. 5 (May 1, 1985): 1570–81. http://dx.doi.org/10.1083/jcb.100.5.1570.

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The majority of the protein mass of HeLa 40S heterogeneous nuclear ribonucleoprotein monoparticles is composed of multiple copies of six proteins that resolve in SDS gels as three groups of doublet bands (A1, A2; B1, B2; and C1, C2) (Beyer, A. L., M. E. Christensen, B. W. Walker, and W. M. LeStourgeon. 1977. Cell. 11: 127-138). We report here that when 40S monoparticles are exposed briefly to ribonuclease, proteins A1, C1, and C2 are solubilized coincidentally with the loss of most premessenger RNA sequences. The remaining proteins exist as tetramers of (A2)3(B1) or pentamers of (A2)3(B1)(B2). The tetramers may reassociate in highly specific ways to form either of two different structures. In 0.1 M salt approximately 12 tetramers (derived from three or four monoparticles) reassemble to form highly regular structures, which may possess dodecahedral symmetry. These structures sediment at 43S, are 20-22 nm in width, and have a mass near 2.3 million. These structures possess 450-500 bases of slowly labeled RNA, which migrates in gels as fragments 200-220 bases in length. In 9 mM salt the tetramers reassociate to form 2.0 M salt-insoluble helical filaments of indeterminant length with a pitch near 60 nm and diameter near 18 nm. If 40S monoparticles are treated briefly with nuclease-free proteases, the same proteins solubilized by nuclease (A1, C1, and C2) are preferentially cleaved. This protein cleavage is associated with the dissociation of most of the heterogeneous nuclear RNA. Proteins A2 and B1 again reassemble to form uniform, globular particles, but these sediment slightly slower than intact monoparticles. These findings indicate that proteins A1, C1, and C2 and most of the premessenger sequences occupy a peripheral position in intact monoparticles and that their homotypic and heterotypic associations are dependent on protein-RNA interactions. Protein cross-linking studies demonstrate that trimers of A1, A2, and C1 exist as the most easily stabilized homotypic association in 40S particles. This supports the 3:1 ratio (via densitometry) of the A and C proteins to the B proteins and indicates that 40S monoparticles are composed of three or four repeating units, each containing 3(A1),3(A2),1(B1),1(B2),3(C1), and 1(C2).

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Hoang, Tung, Ton Huu Phan, Hai Van Tong, and Trung Nam Tran. "Evaluation of Local Black Glutinous Rice Germplasm of Vietnam for Resistance to Bacterial Leaf Blight Disease." Vietnam Journal of Agricultural Sciences 1, no. 3 (February 13, 2019): 240–48. http://dx.doi.org/10.31817/vjas.2018.1.3.05.

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Most rice growing areas frequently encounter the bacterial leaf blight, Xanthomonas oryzae pv oryzae (Xoo). To prevent the disease, development of resistant varieties is considered to be the most economical and environmentally safe solution. In this study, three PCR-based markers, Npb181, RM122, and P3, were used for the identification of the genes Xa4, xa5, and Xa7, respectively, from 56 local black glutinous rice accessions of Vietnam. Phenotypic screening of the accessions for resistance to 10 Xoo strains of North Vietnam, along with IRBB4, IRBB5, and IRBB7 as resistant controls and IR24 as a susceptible control were carried out in the 2016 Autumn season. 19 accessions containing the resistant genes were found, of these, 6 accessions carried Xa4 gene, 6 accessions carried xa5 gene, and 11 accessions carried Xa7 gene. Three accessions carried two resistance genes, viz. Nep do (Xa4 and Xa7), Pau cam (xa5 and Xa7), and Pe lon cam (Xa4 and xa5). Accessions with xa5 and Xa7 alone or with a combination of two genes (Xa4 and xa5, Xa4 and Xa7, or xa5 and Xa7) were resistantto 8-9 Xoo strains (8-9R/0M/1-2S). Accessions containing Xa4 showed resistance to 5-6 strains of Xoo (5-6R/0M/4-5S). Xoo strain No1 (HUA01043) showed the lowest virulence, infecting only 14 accessions (42R/4M/14S). Strains No3 (HUA 0020131-2), No4 (HUA202361), No5 (HUA20212), and No8 (HUA 020083) showed highest virulence, and they each infected more than 40 accessions with 19R/0M/41S, 20R/0M/40S, 16R/4M/40S, and 20R/0M/40S, respectively. These strains can even infect some accessions containing effective resistant genes (Xa4 or Xa7).

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Sergeeva, Olga, Philipp Sergeev, Pavel Melnikov, Tatiana Prikazchikova, Olga Dontsova, and Timofei Zatsepin. "Modification of Adenosine196 by Mettl3 Methyltransferase in the 5’-External Transcribed Spacer of 47S Pre-rRNA Affects rRNA Maturation." Cells 9, no. 4 (April 24, 2020): 1061. http://dx.doi.org/10.3390/cells9041061.

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Ribosome biogenesis is among the founding processes in the cell. During the first stages of ribosome biogenesis, polycistronic precursor of ribosomal RNA passes complex multistage maturation after transcription. Quality control of preribosomal RNA (pre-rRNA) processing is precisely regulated by non-ribosomal proteins and structural features of pre-rRNA molecules, including modified nucleotides. However, many participants of rRNA maturation are still unknown or poorly characterized. We report that RNA m6A methyltransferase Mettl3 interacts with the 5′ external transcribed spacer (5′ETS) of the 47S rRNA precursor and modifies adenosine 196. We demonstrated that Mettl3 knockdown results in the increase of pre-rRNA processing rates, while intracellular amounts of rRNA processing machinery components (U3, U8, U13, U14, and U17 small nucleolar RNA (snoRNA)and fibrillarin, nucleolin, Xrn2, and rrp9 proteins), rRNA degradation rates, and total amount of mature rRNA in the cell stay unchanged. Increased efficacy of pre-rRNA cleavage at A’ and A0 positions led to the decrease of 47S and 45S pre-rRNAs in the cell and increase of mature rRNA amount in the cytoplasm. The newly identified conserved motif DRACH sequence modified by Mettl3 in the 5′-ETS region is found and conserved only in primates, which may suggest participation of m6A196 in quality control of pre-rRNA processing at initial stages demanded by increased complexity of ribosome biogenesis.

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Chiu, Wen-Ling, Susan Wagner, Anna Herrmannová, Laxminarayana Burela, Fan Zhang, Adesh K. Saini, Leoš Valášek, and Alan G. Hinnebusch. "The C-Terminal Region of Eukaryotic Translation Initiation Factor 3a (eIF3a) Promotes mRNA Recruitment, Scanning, and, Together with eIF3j and the eIF3b RNA Recognition Motif, Selection of AUG Start Codons." Molecular and Cellular Biology 30, no. 18 (June 28, 2010): 4415–34. http://dx.doi.org/10.1128/mcb.00280-10.

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ABSTRACT The C-terminal domain (CTD) of the a/Tif32 subunit of budding yeast eukaryotic translation initiation factor 3 (eIF3) interacts with eIF3 subunits j/Hcr1 and b/Prt1 and can bind helices 16 to 18 of 18S rRNA, suggesting proximity to the mRNA entry channel of the 40S subunit. We have identified substitutions in the conserved Lys-Glu-Arg-Arg (KERR) motif and in residues of the nearby box6 element of the a/Tif32 CTD that impair mRNA recruitment by 43S preinitiation complexes (PICs) and confer phenotypes indicating defects in scanning and start codon recognition. The normally dispensable CTD of j/Hcr1 is required for its binding to a/Tif32 and to mitigate the growth defects of these a/Tif32 mutants, indicating physical and functional interactions between these two domains. The a/Tif32 CTD and the j/Hcr1 N-terminal domain (NTD) also interact with the RNA recognition motif (RRM) in b/Prt1, and mutations in both subunits that disrupt their interactions with the RRM increase leaky scanning of an AUG codon. These results, and our demonstration that the extreme CTD of a/Tif32 binds to Rps2 and Rps3, lead us to propose that the a/Tif32 CTD directly stabilizes 43S subunit-mRNA interaction and that the b/Prt1-RRM-j/Hcr1-a/Tif32-CTD module binds near the mRNA entry channel and regulates the transition between scanning-conducive and initiation-competent conformations of the PIC.

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Wang, Zhi-Qiang, Ning Wang, Silvere van der Maarel, Shen-Xing Murong, and Zhi-Ying Wu. "Distinguishing the 4qA and 4qB variants is essential for the diagnosis of facioscapulohumeral muscular dystrophy in the Chinese population." European Journal of Human Genetics 19, no. 1 (August 25, 2010): 64–69. http://dx.doi.org/10.1038/ejhg.2010.143.

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Holtz, Gudrun. "Inclusivism at Qumran." Dead Sea Discoveries 16, no. 1 (2009): 22–54. http://dx.doi.org/10.1163/156851709x395759.

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AbstractWithin Early Judaism the Qumran Community is widely perceived as a strictly exclusivist group. A thorough analysis of Qumran texts, however, reveals, apart from the dominant strand of exclusivism, remarkably clear inclusivist tendencies. In Qumran literature inclusivist tendencies can be seen both in eschatological texts and in materials dealing with the self-understanding of the Qumran Community in historical time. The legal texts discussed basically confirm this pattern: the Community is to separate from Gentiles and from members of those Jewish groups with whom it earlier entertained close relations. At the same time it is to support the poor and the proselytes. Strictly legal statements prohibiting contacts with non-Essene Judaism as such are missing. In the literature discussed inclusivist and exclusivist tendencies have diff erent weight. A pan-Israelite, e.g. inclusivist, perspective can be seen in 4QpNah, 4QFlor, 4QSM and especially in 4QMMT, 1QSa, and CD/4QD whereas in 1QS exclusivist tendencies predominate.

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Huang, Ming-Hui, and Roland T. Rust. "A strategic framework for artificial intelligence in marketing." Journal of the Academy of Marketing Science 49, no. 1 (November 4, 2020): 30–50. http://dx.doi.org/10.1007/s11747-020-00749-9.

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AbstractThe authors develop a three-stage framework for strategic marketing planning, incorporating multiple artificial intelligence (AI) benefits: mechanical AI for automating repetitive marketing functions and activities, thinking AI for processing data to arrive at decisions, and feeling AI for analyzing interactions and human emotions. This framework lays out the ways that AI can be used for marketing research, strategy (segmentation, targeting, and positioning, STP), and actions. At the marketing research stage, mechanical AI can be used for data collection, thinking AI for market analysis, and feeling AI for customer understanding. At the marketing strategy (STP) stage, mechanical AI can be used for segmentation (segment recognition), thinking AI for targeting (segment recommendation), and feeling AI for positioning (segment resonance). At the marketing action stage, mechanical AI can be used for standardization, thinking AI for personalization, and feeling AI for relationalization. We apply this framework to various areas of marketing, organized by marketing 4Ps/4Cs, to illustrate the strategic use of AI.

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Caracelli, Ignez, Julio Zukerman-Schpector, André T. Lousada Machado, Timothy J. Brocksom, M. Lúcia Ferreira, and Edward R. T. Tiekink. "(4R*,4aS*,4bS*,5R*,10aR*)-4-Hydroxy-4a,5-dimethyl-2-(propan-2-yl)-1,4,4a,4b,5,6,7,8,10,10a-decahydrophenanthren-1-one." Acta Crystallographica Section E Structure Reports Online 67, no. 12 (November 16, 2011): o3338. http://dx.doi.org/10.1107/s1600536811048008.

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Caracelli, Ignez, Julio Zukerman-Schpector, André T. Lousada Machado, Timothy J. Brocksom, M. Lúcia Ferreira, and Edward R. T. Tiekink. "(4R,4aS,4bS,7R,10aR)-4-Hydroxy-4a,7-dimethyl-2-(propan-2-yl)-1,4,4a,4b,5,6,7,8,10,10a-decahydrophenanthren-1-one." Acta Crystallographica Section E Structure Reports Online 67, no. 11 (October 29, 2011): o3136. http://dx.doi.org/10.1107/s1600536811044540.

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Yang, Dong Po, and Jian Min Han. "The Study of the Plastic Cover Mold Design and Process Optimization Based on Moldflow." Advanced Materials Research 569 (September 2012): 290–96. http://dx.doi.org/10.4028/www.scientific.net/amr.569.290.

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In this paper, according to the quality problems of the plastic cover such as the difficulty control of the mold temperature, long cooling time, low production efficiency and deformation, it analyses the problems existing in the mold causes and find solutions based on Moldflow as a research tool. By improving the quality of gate position to control the filling quality, redesigning the cooling system to improve cooling efficiency, optimizing molding process to control product quality and increasing wall thickness to eliminate air traps and weld lines guide the design and manufacturing of the new mould. It establishes the gating system and cooling system based on the ASA778T as filling material and the analysis of simplified model. Select the process: the mold surface temperature is 80°C, the melt temperature is 240°C, the mold-open time is 15s, the packing time is 10s, the packing pressure is 80Mpa, injection+packing+cooling time is 45s. This process reduces the molding cycle from 65s to 42s, decreases the maximum deformation in 2.866mm, ensures the product quality, saves the cost and improves the production efficiency.

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Kedersha, Nancy, Samantha Chen, Natalie Gilks, Wei Li, Ira J. Miller, Joachim Stahl, and Paul Anderson. "Evidence That Ternary Complex (eIF2-GTP-tRNAi Met)–Deficient Preinitiation Complexes Are Core Constituents of Mammalian Stress Granules." Molecular Biology of the Cell 13, no. 1 (January 2002): 195–210. http://dx.doi.org/10.1091/mbc.01-05-0221.

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Environmental stress-induced phosphorylation of eIF2α inhibits protein translation by reducing the availability of eIF2-GTP-tRNAiMet, the ternary complex that joins initiator tRNAMet to the 43S preinitiation complex. The resulting untranslated mRNA is dynamically routed to discrete cytoplasmic foci known as stress granules (SGs), a process requiring the related RNA-binding proteins TIA-1 and TIAR. SGs appear to be in equilibrium with polysomes, but the nature of this relationship is obscure. We now show that most components of the 48S preinitiation complex (i.e., small, but not large, ribosomal subunits, eIF3, eIF4E, eIF4G) are coordinately recruited to SGs in arsenite-stressed cells. In contrast, eIF2 is not a component of newly assembled SGs. Cells expressing a phosphomimetic mutant (S51D) of eIF2α assemble SGs of similar composition, confirming that the recruitment of these factors is a direct consequence of blocked translational initiation and not due to other effects of arsenite. Surprisingly, phospho-eIF2α is recruited to SGs that are disassembling in cells recovering from arsenite-induced stress. We discuss these results in the context of a translational checkpoint model wherein TIA and eIF2 are functional antagonists of translational initiation, and in which lack of ternary complex drives SG assembly.

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Treat, Tod. "4Bs or not 4Bs: Bricks, bytes, brains, and bandwidth." New Directions for Community Colleges 2011, no. 154 (June 2011): 5–15. http://dx.doi.org/10.1002/cc.442.

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Journal articles on the topic '4QS'

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