Journal articles: 'Functional ATPG'

1

Ashar, P., and S. Malik. "Functional timing analysis using ATPG." IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 14, no. 8 (1995): 1025–30. http://dx.doi.org/10.1109/43.402501.

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Michael, M., and S. Tragoudas. "ATPG tools for delay faults at the functional level." ACM Transactions on Design Automation of Electronic Systems 7, no. 1 (January 2002): 33–57. http://dx.doi.org/10.1145/504914.504916.

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Hobeika, Christelle, Claude Thibeault, and Jean-Francois Boland. "Functional Constraint Extraction From Register Transfer Level for ATPG." IEEE Transactions on Very Large Scale Integration (VLSI) Systems 23, no. 2 (February 2015): 407–12. http://dx.doi.org/10.1109/tvlsi.2014.2309439.

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Barriuso-Iglesias, Mónica, Carlos Barreiro, Fabio Flechoso, and Juan F. Martín. "Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH." Microbiology 152, no. 1 (January 1, 2006): 11–21. http://dx.doi.org/10.1099/mic.0.28383-0.

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Corynebacterium glutamicum, a soil Gram-positive bacterium used for industrial amino acid production, was found to grow optimally at pH 7·0–9·0 when incubated in 5 litre fermenters under pH-controlled conditions. The highest biomass was accumulated at pH 9·0. Growth still occurred at pH 9·5 but at a reduced rate. The expression of the pH-regulated F0F1 ATPase operon (containing the eight genes atpBEFHAGDC) was induced at alkaline pH. A 7·5 kb transcript, corresponding to the eight-gene operon, was optimally expressed at pH 9·0. The same occurred with a 1·2 kb transcript corresponding to the atpB gene. RT-PCR studies confirmed the alkaline pH induction of the F0F1 operon and the existence of the atpI gene. The atpI gene, located upstream of the F0F1 operon, was expressed at a lower level than the polycistronic 7·5 kb mRNA, from a separate promoter (P-atp1). Expression of the major promoter of the F0F1 operon, designated P-atp2, and the P-atp1 promoter was quantified by coupling them to the pET2 promoter-probe vector. Both P-atp1 and P-atp2 were functional in C. glutamicum and Escherichia coli. Primer extension analysis identified one transcription start point inside each of the two promoter regions. The P-atp1 promoter fitted the consensus sequence of promoters recognized by the vegetative σ factor of C. glutamicum, whereas the −35 and −10 boxes of P-atp2 fitted the consensus sequence for σ H-recognized Mycobacterium tuberculosis promoters CC/GGGA/GAC 17–22 nt C/GGTTC/G, known to be involved in expression of heat-shock and other stress-response genes. These results suggest that the F0F1 operon is highly expressed at alkaline pH, probably using a σ H RNA polymerase.

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Topisirovic, Dragan. "Advances in VLSI testing at MultiGb per second rates." Serbian Journal of Electrical Engineering 2, no. 1 (2005): 43–55. http://dx.doi.org/10.2298/sjee0501043t.

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Today's high performance manufacturing of digital systems requires VLSI testing at speeds of multigigabits per second (multiGbps). Testing at Gbps needs high transfer rates among channels and functional units, and requires readdressing of data format and communication within a serial mode. This implies that a physical phenomena-jitter, is becoming very essential to tester operation. This establishes functional and design shift, which in turn dictates a corresponding shift in test and DFT (Design for Testability) methods. We, here, review various approaches and discuss the tradeoffs in testing actual devices. For industry, volume-production stage and testing of multigigahertz have economic challenges. A particular solution based on the conventional ATE (Automated Test Equipment) resources, that will be discussed, allows for accurate testing of ICs with many channels and this systems can test ICs at 2.5 Gbps over 144 cannels, with extensions planned that will have test rates exceeding 5 Gbps. Yield improvement requires understanding failures and identifying potential sources of yield loss. This text focuses on diagnosing of random logic circuits and classifying faults. An interesting scan-based diagnosis flow, which leverages the ATPG (Automatic Test Pattern Generator) patterns originally generated for fault coverage, will be described. This flow shows an adequate link between the design automation tools and the testers, and a correlation between the ATPG patterns and the tester failure reports.

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Arekapudi, Srikanth, Fei Xin, Jinzheng Peng, and Ian G. Harris. "ATPG for Timing Errors in Globally Asynchronous Locally Synchronous Systems." Journal of Circuits, Systems and Computers 12, no. 03 (June 2003): 305–32. http://dx.doi.org/10.1142/s0218126603000775.

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Globally Asynchronous, Locally Synchronous (GALS) systems are now commonplace in many cost-critical and life-critical applications, thus motivating the need for a systematic approach to verify functionality. The complexity of the verification problem for large heterogeneous GALS systems necessitates the development of simulation-based validation approaches to uniformly validate hardware, software, and their interaction. GALS systems are comprised of several processes which may be mapped to different hardware and software components and communicate through asynchronous interfaces. Communication between these processes must be verified to ensure that the system is working correctly. Previous work focuses on checking the correctness of individual processes rather than communication between multiple processes. Timing errors may cause a signal to have an incorrect value for a short time period. Timing errors can cause a problem in GALS systems if the value of a signal with a timing error is used while is has an incorrect value. This paper presents an automatic test pattern generation (ATPG) tool to generate tests for timing-induced functional errors.

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Veneris, Andreas, Robert Chang, Magdy S. Abadir, and Sep Seyedi. "Functional Fault Equivalence and Diagnostic Test Generation in Combinational Logic Circuits Using Conventional ATPG." Journal of Electronic Testing 21, no. 5 (October 2005): 495–502. http://dx.doi.org/10.1007/s10836-005-1543-z.

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Arunachalam, Ravishankar, Ronald DeShawn Blanton, and Lawrence T. Pileggi. "Accurate Coupling-centric Timing Analysis Incorporating Temporal and Functional Isolation." VLSI Design 15, no. 3 (January 1, 2002): 605–18. http://dx.doi.org/10.1080/1065514021000012228.

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Neighboring line switching can contribute to a large portion of the delay of a line for today's deep submicron designs. The impact of this switching on delay is usually estimated by scaling the coupling capacitances (often by a factor of 2) and modeling them as grounded. This simple approach has been shown to be overly pessimistic in some cases, while somewhat optimistic in others. Apart from the delay modeling inaccuracies, the temporal and functional isolation of the aggressors can contribute to the pessimism. This paper introduces TACO, a timing analysis approach that addresses both these issues. TACO captures the provably worst-and best-case delays as a function of the timing-window inputs to the gates. We then present a comprehensive ATPG-based approach that uses functional information to identify valid interactions between coupled lines. Our algorithm accounts for glitches on aggressors that can be caused by static and dynamic hazards in the circuit. Results on industrial examples and benchmark circuits show the value of our approach.

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Lv, Zhao, Shuming Chen, and Yaohua Wang. "Simulation-Based Hardware Verification with a Graph-Based Specification." Mathematical Problems in Engineering 2018 (2018): 1–10. http://dx.doi.org/10.1155/2018/6398616.

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Simulation-based verification continues to be the primary technique for hardware verification due to its scalability and ease of use; however, it lacks exhaustiveness. Although formal verification techniques can exhaustively prove functional correctness, they are limited in terms of the scale of their design due to the state-explosion problem. Alternatively, semiformal approaches can involve a compromise between scalability, exhaustiveness, and resource costs. Therefore, we propose an event-driven flow graph-based specification, which can describe the cycle-accurate functional behaviors without the exploration of whole state space. To efficiently generate input sequences according to the proposed specification, we introduce a functional automatic test pattern generation (ATPG) approach, which involves the proposed intelligent redundancy-reduction strategy to solve problems of random test vectors. We also proposed functional coverage criterion based on the formal specification to support a more reliable measure of verification. We implement a verification platform based on the proposed semiformal approach and compare the proposed semiformal approach with the constrained randomized test (CRT) approach. The experiment results show that the proposed semiformal verification method ensures a more exhaustive and effective exploration of the functional correctness of designs under verification (DUVs).

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Zhao, Zhe, Lauren J. Eberhart, Lisa H. Orfe, Shao-Yeh Lu, Thomas E. Besser, and Douglas R. Call. "Genome-Wide Screening Identifies Six Genes That Are Associated with Susceptibility to Escherichia coli Microcin PDI." Applied and Environmental Microbiology 81, no. 20 (July 24, 2015): 6953–63. http://dx.doi.org/10.1128/aem.01704-15.

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ABSTRACTThe microcin PDI inhibits a diverse group of pathogenicEscherichia colistrains. Coculture of a single-gene knockout library (BW25113;n= 3,985 mutants) against a microcin PDI-producing strain (E. coli25) identified six mutants that were not susceptible (ΔatpA, ΔatpF, ΔdsbA, ΔdsbB, ΔompF, and ΔompR). Complementation of these genes restored susceptibility in all cases, and the loss of susceptibility was confirmed through independent gene knockouts inE. coliO157:H7 Sakai. Heterologous expression ofE. coliompFconferred susceptibility toSalmonella entericaandYersinia enterocoliticastrains that are normally unaffected by microcin PDI. The expression of chimeric OmpF and site-directed mutagenesis revealed that the K47G48N49region within the first extracellular loop ofE. coliOmpF is a putative binding site for microcin PDI. OmpR is a transcriptional regulator forompF, and consequently loss of susceptibility by the ΔompRstrain most likely is related to this function. Deletion of AtpA and AtpF, as well as AtpE and AtpH (missed in the original library screen), resulted in the loss of susceptibility to microcin PDI and the loss of ATP synthase function. Coculture of a susceptible strain in the presence of an ATP synthase inhibitor resulted in a loss of susceptibility, confirming that a functional ATP synthase complex is required for microcin PDI activity. Intransexpression ofompFin the ΔdsbAand ΔdsbBstrains did not restore a susceptible phenotype, indicating that these proteins are probably involved with the formation of disulfide bonds for OmpF or microcin PDI.

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Muthukrishnan, Prathiba, and Sivanantham Sathasivam. "A Technical Survey on Delay Defects in Nanoscale Digital VLSI Circuits." Applied Sciences 12, no. 18 (September 10, 2022): 9103. http://dx.doi.org/10.3390/app12189103.

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As technology scales down, digital VLSI circuits are prone to many manufacturing defects. These defects may result in functional and delay-related circuit failures. The number of test escapes grows when technology is downscaled. Small delay defects (SDDs) and hidden delay defects (HDDs) are of critical importance in industries today since they are the source of most test escapes and reliability problems. Improving test quality and creating new test methods, algorithms, and test designs requires a comprehensive study of these delay defects. This article reviews the effect and impact of SDD and HDD in logic circuits. It also analyzes the relevant fault models, automatic test pattern generation (ATPG) methods, faster-than-at-speed testing (FAST), cell-aware (CA) based delay tests, test quality metrics, diagnosis of SDDs and HDDs, and commercially available Electronic Design Automation (EDA) tools. Based on the analysis, the benefits and drawbacks of several accessible approaches are addressed.

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Smith, Christopher P., and Peter E. Thorsness. "Formation of an Energized Inner Membrane in Mitochondria with a γ-Deficient F1-ATPase." Eukaryotic Cell 4, no. 12 (December 2005): 2078–86. http://dx.doi.org/10.1128/ec.4.12.2078-2086.2005.

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ABSTRACT Eukaryotic cells require mitochondrial compartments for viability. However, the budding yeast Saccharomyces cerevisiae is able to survive when mitochondrial DNA suffers substantial deletions or is completely absent, so long as a sufficient mitochondrial inner membrane potential is generated. In the absence of functional mitochondrial DNA, and consequently a functional electron transport chain and F1Fo-ATPase, the essential electrical potential is maintained by the electrogenic exchange of ATP4− for ADP3− through the adenine nucleotide translocator. An essential aspect of this electrogenic process is the conversion of ATP4− to ADP3− in the mitochondrial matrix, and the nuclear-encoded subunits of F1-ATPase are hypothesized to be required for this process in vivo. Deletion of ATP3, the structural gene for the γ subunit of the F1-ATPase, causes yeast to quantitatively lose mitochondrial DNA and grow extremely slowly, presumably by interfering with the generation of an energized inner membrane. A spontaneous suppressor of this slow-growth phenotype was found to convert a conserved glycine to serine in the β subunit of F1-ATPase (atp2-227). This mutation allowed substantial ATP hydrolysis by the F1-ATPase even in the absence of the γ subunit, enabling yeast to generate a twofold greater inner membrane potential in response to ATP compared to mitochondria isolated from yeast lacking the γ subunit and containing wild-type β subunits. Analysis of the suppressing mutation by blue native polyacrylamide gel electrophoresis also revealed that the α3β3 heterohexamer can form in the absence of the γ subunit.

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Bergamin, G., A. Caratelli, D. Ceresa, K. Kloukinas, S. Scarfì, and A. Nookala. "Study, implementation and testing of radiation tolerant design for testability solutions for CMS OT FE ASICs." Journal of Instrumentation 17, no. 04 (April 1, 2022): C04009. http://dx.doi.org/10.1088/1748-0221/17/04/c04009.

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Abstract The MPA and SSA development is approaching the production phase with an approximate volume of more than 200k ASICs, corresponding to 1200 wafers. The limited manufacturing yield requires testing strategies able to identify defective units and guarantee the correct functionality of the tracker modules. This contribution presents innovative methods to replace the currently used functional tests for the digital part of the ASICs, showing limited testing accuracy and long testing time. The proposed solution exploits the concept of structural test and new testing algorithms such as Automatic Test Pattern Generation (ATPG) for general digital logic and March for memory elements. Design for Testability (DFT) hardware is integrated on chip to test SRAM memories, peripheral logic and MPA pixel array, providing internal control and observation points for the implementation of the those algorithms. Particular attention is given to power increase, timing and placement impact as well as radiation tolerance of the introduced circuitry, which must be fully transparent during the normal operation of the chip. A faster and more accurate testing approach is presented, from design methodology to implementation choices and silicon results, for a reliable and cost effective testing procedure.

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Gowda, Madhura Rame, and Jamuna Jamuna. "Fault simulation for design for testability inserted designs." Indonesian Journal of Electrical Engineering and Computer Science 29, no. 2 (February 1, 2023): 658. http://dx.doi.org/10.11591/ijeecs.v29.i2.pp658-668.

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<p>Systematic design for testability (DFT) is a technique to enhance the testability of design so that it is further organized and self-regulating. The objective of systematic DFT is to enhance a circuit's operability and evidence. This can be performed in a variety of ways. The scan pattern method is the extremely predominant, and it modifies the design's internal sequential circuitry. In this manuscript, frequently used industry standard functional register-transfer level (RTL) designs are chosen. Structured DFT approach is adopted to do scan insertion and automatic test pattern generation (ATPG) to enhance the testability. Proposed methodology provides the controllability and observability for the clocks and reset used in chosen RTL designs by eliminating S rule and D rule violations by adding test logic. Also able to insert stuck at faults and achieve fault coverage of 97.78% and test coverage of 99.26% for DFT architecture for Wallace tree multiplier design, and found different classes of faults as testable and untestable faults and also performed fault simulation for the intended designs to detect fault from the created deterministic patterns.</p>

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Seghezzi, Nicolas, Emmanuelle Darbon, Cécile Martel, Michelle David, Clara Lejeune, Catherine Esnault, and Marie-Joelle Virolle. "The Generation of an Artificial ATP Deficit Triggers Antibiotic Production in Streptomyces lividans." Antibiotics 11, no. 9 (August 27, 2022): 1157. http://dx.doi.org/10.3390/antibiotics11091157.

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In most Streptomyces species, antibiotic production is triggered in a condition of phosphate limitation, a condition that is known to be correlated with a low intracellular ATP content compared to growth in a condition of phosphate proficiency. This observation suggests that a low ATP content might be a direct trigger of antibiotic biosynthesis. In order to test this hypothesis, we introduced into the model strain Streptomyces lividans, a functional and a non-functional ATPase cloned into the replicative vector pOSV206 and expressed under the control of the strong ErmE* promoter. The functional ATPase was constituted by the α (AtpA), β (AtpB) and γ (AtpD) sub-units of the native F1 part of the ATP synthase of S. lividans that, when separated from the membrane-bound F0 part, bears an ATPase activity. The non-functional ATPase was a mutated version of the latter, bearing a 12 amino acids deletion encompassing the active site of the AtpD sub-unit. S. lividans was chosen to test our hypothesis since this strain hardly produces any antibiotics. However, it possesses the same biosynthetic pathways of various specialized metabolites as S. coelicolor, a phylogenetically closely related strain that produces these metabolites in abundance. Our results demonstrated that the over-expression of the functional ATPase, but not that of its mutated version, indeed correlated with the production of the bioactive metabolites of the CDA, RED and ACT clusters. These results confirmed the long known and mysterious link existing between a phosphate limitation leading to an ATP deficit and the triggering of antibiotic biosynthesis. Based on this work and the previous published results of our group, we propose an entirely novel conception of the nature of this link.

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Prikryl, Jana, Margarita Rojas, Gadi Schuster, and Alice Barkan. "Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein." Proceedings of the National Academy of Sciences 108, no. 1 (December 20, 2010): 415–20. http://dx.doi.org/10.1073/pnas.1012076108.

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Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that bind RNA and modulate organellar RNA metabolism. The mechanisms underlying the functions attributed to PPR proteins are unknown. We describe in vitro studies of the maize protein PPR10 that clarify how PPR10 modulates the stability and translation of specific chloroplast mRNAs. We show that recombinant PPR10 bound to its native binding site in the chloroplast atpI–atpH intergenic region (i) blocks both 5′→3′ and 3′→ 5 exoribonucleases in vitro; (ii) is sufficient to define the native processed atpH mRNA 5′-terminus in conjunction with a generic 5′→3′ exoribonuclease; and (iii) remodels the structure of the atpH ribosome-binding site in a manner that can account for PPR10’s ability to enhance atpH translation. In addition, we show that the minimal PPR10-binding site spans 17 nt. We propose that the site-specific barrier and RNA remodeling activities of PPR10 are a consequence of its unusually long, high-affinity interface with single-stranded RNA, that this interface provides a functional mimic to bacterial small RNAs, and that analogous activities underlie many of the biological functions that have been attributed to PPR proteins.

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Di Mauro, Stefania, Alessandra Scamporrino, Agnese Filippello, Maurizio Di Marco, Maria Teresa Di Martino, Francesca Scionti, Antonino Di Pino, et al. "Mitochondrial RNAs as Potential Biomarkers of Functional Impairment in Diabetic Kidney Disease." International Journal of Molecular Sciences 23, no. 15 (July 25, 2022): 8198. http://dx.doi.org/10.3390/ijms23158198.

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Type 2 diabetes and renal damage are strictly linked. The progressive increase in T2D incidence has stimulated the interest in novel biomarkers to improve the diagnostic performance of the commonly utilized markers such as albuminuria and eGFR. Through microarray method, we analyzed the entire transcriptome expressed in 12 serum samples of diabetic patients, six without DKD and six with DKD; the downregulation of the most dysregulated transcripts was validated in a wider cohort of 69 patients by qPCRs. We identified a total of 33 downregulated transcripts. The downregulation of four mitochondrial messenger RNAs (MT-ATP6, MT-ATP8, MT-COX3, MT-ND1) and other two transcripts (seysnoy, skerdo) was validated in patients with eGFR stage G3 versus G2 and G1. The four messenger RNAs correlated with creatinine and eGFR stages, while seysnoy and skerdo were associated with white blood cell values. All transcripts correlated also with Blood Urea Nitrogen. The four mitochondrial messenger RNAs had a high diagnostic performance in G3 versus G2 discrimination, with AUC values above 0.8. The most performant transcript was MT-ATP6, with an AUC of 0.846; sensitivity = 90%, specificity = 76%, p-value = 7.8 × 10−5. This study led to the identification of a specific molecular signature of DKD, proposing the dosage of RNAs, especially mitochondrial RNAs, as noninvasive biomarkers of diabetes complication.

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Hejzlarová, Kateřina, Vilma Kaplanová, Hana Nůsková, Nikola Kovářová, Pavel Ješina, Zdeněk Drahota, Tomáš Mráček, Sara Seneca, and Josef Houštěk. "Alteration of structure and function of ATP synthase and cytochrome c oxidase by lack of Fo-a and Cox3 subunits caused by mitochondrial DNA 9205delTA mutation." Biochemical Journal 466, no. 3 (March 6, 2015): 601–11. http://dx.doi.org/10.1042/bj20141462.

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Mutations in the MT-ATP6 gene are frequent causes of severe mitochondrial disorders. Typically, these are missense mutations, but another type is represented by the 9205delTA microdeletion, which removes the stop codon of the MT-ATP6 gene and affects the cleavage site in the MT-ATP8/MT-ATP6/MT-CO3 polycistronic transcript. This interferes with the processing of mRNAs for the Atp6 (Fo-a) subunit of ATP synthase and the Cox3 subunit of cytochrome c oxidase (COX). Two cases described so far presented with strikingly different clinical phenotypes–mild transient lactic acidosis or fatal encephalopathy. To gain more insight into the pathogenic mechanism, we prepared 9205delTA cybrids with mutation load ranging between 52 and 99% and investigated changes in the structure and function of ATP synthase and the COX. We found that 9205delTA mutation strongly reduces the levels of both Fo-a and Cox3 proteins. Lack of Fo-a alters the structure but not the content of ATP synthase, which assembles into a labile, ∼60 kDa smaller, complex retaining ATP hydrolytic activity but which is unable to synthesize ATP. In contrast, lack of Cox3 limits the biosynthesis of COX but does not alter the structure of the enzyme. Consequently, the diminished mitochondrial content of COX and non-functional ATP synthase prevent most mitochondrial ATP production. The biochemical effects caused by the 9205delTA microdeletion displayed a pronounced threshold effect above ∼90% mutation heteroplasmy. We observed a linear relationship between the decrease in subunit Fo-a or Cox3 content and the functional presentation of the defect. Therefore we conclude that the threshold effect originated from a gene–protein level.

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Becker-Dettling, Fiona, Robert Dalla-Pozza, Adelheid Kley, Esther M. Maier, and Stephanie Regenauer-Vandewiele. "Infantile Mitochondrial Cardiomyopathy – A Case Report Presenting a Rare Cause for Hypertrophic Cardiomyopathy." Clinical Cardiology and Cardiovascular Interventions 5, no. 5 (May 16, 2022): 01–06. http://dx.doi.org/10.31579/2641-0419/255.

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Infantile hypertrophic cardiomyopathy (HCM) comprises a group of rare and heterogeneous diseases and is the second most common cause of cardiomyopathy in childhood and adolescents. In general, the muscular hypertrophy results in histological and functional disorder. The prognosis depends on the underlying aetiology. However, HCM represents a high risk of mortality especially in neonates. Rarely, mitochondrial dysfunction is accountable for HCM. Here we describe a case of a rapidly progressive infantile HCM caused by complex V deficiency due to overlapping mt mutations in ATP6 and ATP8 with lethal course in a premature neonate suggesting early genetic testing in risk groups to clarify differential diagnosis, and determine thereby prognosis and rational therapy options.

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Li, Ying, Qilu Song, Jialin Guo, Yulong Song, Xinhong Chen, and Gaisheng Zhang. "Comparative Analysis of Mitochondrial Genomes between the B-Type Cytoplasmic Male Sterility Line and Its Maintainer Line in Wheat." Agronomy 12, no. 4 (March 30, 2022): 851. http://dx.doi.org/10.3390/agronomy12040851.

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Cytoplasmic male sterility (CMS) is a complex phenomenon in plants, rendering them unable to produce functional pollen. In general, this is caused by an abnormal or dysfunctional mitochondrial genome. In wheat, however, the systematic structural characteristics of the mitochondrial genome from the CMS line, vis-à-vis its maintainer line, are rarely reported. Here, we identified the morphological characteristics, sequenced, assembled, and characterized the complete mitogenomes of the wheat B-type CMS line (B) and its maintainer line (YS9). The morphological results indicated that the B likely undergoes binucleate microspore abortion. The B and YS9 genomes were assembled into a typical circular molecule 452,794 and 452,453 bp in length, respectively, comprising 34 protein-coding genes (PCGs), 3 ribosomal RNA genes (rRNAs), and 16 transfer RNA genes (tRNAs). The codon usage analysis revealed leucine (Leu) and serine (Ser) as the most frequently used amino acid residues in the B and YS9 mitochondrial proteins. In particular, we uncovered a specific ORF2718, whose length of 501 bp was more 30 bp than that of the atp8 gene in the B genome, which perhaps could affect normal function of ATP8. Further, the existence of SNPs at the atp6 gene is probably associated with the CMS mechanism. This study suggests that sequencing and comparing the genomic features of the B and YS9 mitogenomes provides not only an important opportunity to conduct further genomic breeding studies, but also valuable information for future evolutionary and molecular studies of CMS in wheat.

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Rothenberg, M., and M. R. Hanson. "A functional mitochondrial ATP synthase proteolipid gene produced by recombination of parental genes in a petunia somatic hybrid." Genetics 118, no. 1 (January 1, 1988): 155–61. http://dx.doi.org/10.1093/genetics/118.1.155.

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Abstract A novel ATP synthase subunit 9 gene (atp9) was identified in the mitochondrial genome of a Petunia somatic hybrid line (13-133) which was produced from a fusion between Petunia lines 3688 and 3704. The novel gene was generated by intergenomic recombination between atp9 genes from the two parental plant lines. The entire atp9 coding region is represented on the recombinant gene. Comparison of gene sequences indicate that the 5' transcribed region is contributed by an atp9 gene from 3704 and the 3' transcribed region is contributed by an atp9 gene from 3688. The recombinant atp9 gene is transcriptionally active. The location of the 5' and 3' transcript termini are conserved with respect to the parental genes, resulting in the production of hybrid transcripts.

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Lauri, Natalia, Zaher Bazzi, Cora L. Alvarez, María F. Leal Denis, Julieta Schachter, Vanesa Herlax, Mariano A. Ostuni, and Pablo J. Schwarzbaum. "ATPe Dynamics in Protozoan Parasites. Adapt or Perish." Genes 10, no. 1 (December 27, 2018): 16. http://dx.doi.org/10.3390/genes10010016.

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In most animals, transient increases of extracellular ATP (ATPe) are used for physiological signaling or as a danger signal in pathological conditions. ATPe dynamics are controlled by ATP release from viable cells and cell lysis, ATPe degradation and interconversion by ecto-nucleotidases, and interaction of ATPe and byproducts with cell surface purinergic receptors and purine salvage mechanisms. Infection by protozoan parasites may alter at least one of the mechanisms controlling ATPe concentration. Protozoan parasites display their own set of proteins directly altering ATPe dynamics, or control the activity of host proteins. Parasite dependent activation of ATPe conduits of the host may promote infection and systemic responses that are beneficial or detrimental to the parasite. For instance, activation of organic solute permeability at the host membrane can support the elevated metabolism of the parasite. On the other hand ecto-nucleotidases of protozoan parasites, by promoting ATPe degradation and purine/pyrimidine salvage, may be involved in parasite growth, infectivity, and virulence. In this review, we will describe the complex dynamics of ATPe regulation in the context of protozoan parasite–host interactions. Particular focus will be given to features of parasite membrane proteins strongly controlling ATPe dynamics. This includes evolutionary, genetic and cellular mechanisms, as well as structural-functional relationships.

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Wang, Jun, Jia-He Chen, Zhen-Chong Chen, Zhen-Yi Wu, Xiao-Na Zhong, and Jing-Ping Ke. "The LiTFSI/COFs Fiber as Separator Coating with Bifunction of Inhibition of Lithium Dendrite and Shuttle Effect for Li-SeS2 Battery." Coatings 12, no. 2 (February 21, 2022): 289. http://dx.doi.org/10.3390/coatings12020289.

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The safety problem caused by lithium dendrite of lithium metal anode and the rapid capacity decay problem caused by the shuttle effect of polysulfide and polyselenide during the charge and discharge of selenium disulfide cathode limit the application of lithium selenium disulfide batteries significantly. Here, a fibrous ATFG-COF, containing rich carbonyl and amino functional groups, was applied as the separator coating layer. Density Functional Theory (DFT) theoretical calculations and experimental results showed that the abundant carbonyl group in ATFG-COF had a positive effect on lithium ions, and the amino group formed hydrogen bonds with bis ((trifluoromethyl) sulfonyl) azanide anionics (TFSI−), which fixed TFSI− in the channel, so as to improve the transfer number of lithium ions and narrow the channels. Therefore, ATFG-COF fiber coating can not only form a rapid and uniform lithium-ion flow on the lithium anode to inhibit the growth of lithium dendrites, but also effectively screen polysulfide and polyselenide ions to suppress the shuttle effect. The Li-SeS2 cell with ATFG-COF/polypropylene (ATFG-COF/PP) separator exhibited good cycle stability at 0.5 C and maintained a specific capacity of 509 mAh/g after 200 cycles. Our work provides insights into the design of dual-function separators with high-performance batteries.

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Palumbo, Fabio, Nicola Vitulo, Alessandro Vannozzi, Gabriele Magon, and Gianni Barcaccia. "The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions." International Journal of Molecular Sciences 21, no. 13 (June 30, 2020): 4664. http://dx.doi.org/10.3390/ijms21134664.

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Cytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6−, the putative mutant copy with a 300 bp truncation at the 5’-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6+) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6+ copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6+ is expressed only in MF samples, while apt6− mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6− could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility.

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Lin, Ping, Hengfu Yin, Kailiang Wang, Haidong Gao, Lei Liu, and Xiaohua Yao. "Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species." Biomolecules 12, no. 10 (October 13, 2022): 1474. http://dx.doi.org/10.3390/biom12101474.

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Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.

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Aleshkina, G., M. Pugacheva, and L. Bardenshteyn. "Negative symptoms of schizophrenia in patients with acute and transient psychotic disorders." European Psychiatry 64, S1 (April 2021): S802. http://dx.doi.org/10.1192/j.eurpsy.2021.2121.

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IntroductionThe ICD-10 acute and transient psychotic disorders (ATPD, F23) without symptoms of schizophrenia are considered predominantly reactive psychotic disorders or affective pathology. However, negative symptoms of schizophrenia may be revealed in some of these cases after the psychotic reduction.ObjectivesTo investigate the association between the developmental characteristics of psychosis and the negative symptoms detection after the psychotic reduction of ATPD without symptoms of schizophrenia.Methods68 adult inpatients with ATPD without symptoms of schizophrenia (F23.0) were examined. Negative symptoms were assessed with the PANSS negative symptom subscale (PANSS-NSS). The sample was divided into two groups: with PANSS-NSS score>14 (n=12) and with PANSS-NSS score≤14 (n=56), respectively. Clinical-psychopathological, psychometric and statistical methods were applied.ResultsThe results of the study are presented in Table 1.Table 1. The ATPD developmental featuresFeaturesThe 1st group (n=12)The 2nd group (n=56)Pearson’s contingency coefficient (C)Males7 (58,3%)37 (66,1%)0.062Females5 (41,7%)19 (33,9%)0.062Mean age of psychotic onset, years (М±m)24,9±10,530,8±10,2-Family history of schizophrenia*4 (33,3%)1 (1,8%)0.418Poor premorbid social adaptation*5 (41,7%)00.520Prodromal functional decline*9 (75,0%)4 (7,1%)0.550Prodromal non-psychotic symptoms9 (75,0%)30 (53,6%)0.163Associated acute stress4 (33,3%)27 (48,2%)0.113*p<0,001ConclusionsThe probability of negative symptoms detection in ATPD without symptoms of schizophrenia is relatively strongly associated with the family history of schizophrenia, poor premorbid social adaptation and functional decline prior to the psychotic onset.DisclosureNo significant relationships.

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Pizzo, P., M. Murgia, A. Zambon, P. Zanovello, V. Bronte, D. Pietrobon, and F. Di Virgilio. "Role of P2z purinergic receptors in ATP-mediated killing of tumor necrosis factor (TNF)-sensitive and TNF-resistant L929 fibroblasts." Journal of Immunology 149, no. 10 (November 15, 1992): 3372–78. http://dx.doi.org/10.4049/jimmunol.149.10.3372.

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Abstract Two closely related cell lines were characterized in their responses to extracellular ATP (ATPo): the fibroblast cell line L929 and a TNF-resistant variant L929/R. Both lines showed ATPo-activated increases in intracellular Ca2+, inward current, and sustained depolarization of the plasma membrane, cell responses compatible with activation of purinergic receptors of the P2y, P2x, or P2z subtype; however, only the L929/R variant was susceptible to ATPo-dependent early permeabilization of the plasma membrane to hydrophilic solutes of M(r) below 900, a response uniquely caused by the activation of P2z receptors. Both cell types were susceptible to the cytotoxic effect of ATPo, but killing of the L929/R variant required much shorter incubations in the presence of this nucleotide. Morphologic examination of ATPo-challenged L929 and L929/R cells showed that cell death occurred by two alternative mechanisms: colloido-osmotic lysis or apoptosis. Occurrence of apoptosis was confirmed by agarose gel analysis of cellular DNA. Although ATPo caused a fast mobilization of intracellular Ca2+, neither colloido-osmotic lysis nor apoptosis were Ca2+ dependent. Our results show that the L929/R variant, but not the L929 parental fibroblast cell line, expresses functional purinergic receptors of the P2z subtype. The presence of P2z receptors confers to L929/R cells enhanced susceptibility to ATPo-mediated cytotoxicity.

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Jóźwiak, Lech, Aleksander Ślusarczyk, and Marek Perkowski. "Term Trees in Application to an Effective and Efficient ATPG for AND–EXOR and AND–OR Circuits." VLSI Design 14, no. 1 (January 1, 2002): 107–22. http://dx.doi.org/10.1080/10655140290009837.

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A compact data representation, in which the typically required operations are performed rapidly, and effective and efficient algorithms that work on these representations are the essential elements of a successful CAD tool. The objective of this paper is to present a new data representation—term trees (TTs)—and to discuss its application for an effective and efficient structural automatic test-pattern generation (ATPG). Term trees are decision diagrams similar to BDDs that are particularly suitable for structure representation of AND–OR and AND–EXOR circuits. In the paper, a flexible algorithm for minimum term-tree construction is discussed and an effective and efficient algorithm for ATPG for AND–EXOR and AND–OR circuits is proposed. The term trees can be used for many other purposes in logic design and in other areas—for all purposes where compact representation and efficient manipulation of term sets is important. The presented experimental results show that term trees are indeed a compact data representation allowing fast manipulations. They form a good base for algorithms considering the function's and circuit's term structures.

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Al-Dakhil, Mohammed, Salem Alghamdi, Hussein Migdadi, Muhammad Afzal, and Ahmed Abdelrahim Ali. "Morphological Characterization and DNA Barcoding of Duckweed Species in Saudi Arabia." Plants 10, no. 11 (November 12, 2021): 2438. http://dx.doi.org/10.3390/plants10112438.

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Duckweeds, or Lemnaceae, are widespread aquatic plants. Morphology-based identification of duckweed species is difficult because of their structural complexity. Hence, molecular tools provide significant advantages for characterizing and selecting species or clones for sustainable commercial use. In this study, we collected and characterized ten duckweed isolates from nine different regions in Saudi Arabia (SA). Based on the morphological characterization and phylogenetic analysis of intergenic spacer sequences of chloroplast DNA using six barcoding markers, the clones were classified into three genera, represented by seven species: Lemna gibba L., Lemna minor L., Lemna japonica Landolt, Lemna aequinoctialis Welw., Lemna perpusilla Torr., Spirodela polyryiza (L.) Schleid., and Landoltia punctate G. Mey. Lemna gibba was revealed to be a distinct dominant duckweed species in many regions of SA. Five barcoding markers showed that L. gibba, L. minor, and L. punctata were the most widely distributed species in the country. However, L. punctata, L. perpusilla, and S. polyryiza were the dominant species in the Al-Qassim, Madinah-1, and Madinah-2 regions, respectively. Moreover, the morphological traits revealed variations for these clones, relative to other studied duckweed clones. According to the results obtained in this study, three out of six plastid markers (trnH-psbA, matK, and atpF-atpH) helped to identify the dominant duckweed species in Saudi Arabia. Further evaluation based on adaptability, molecular genetic studies, and functional genomics is needed for these species to be used at the commercial level in Saudi Arabia.

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Kuhn, Josef, Ulrike Tengler, and Stefan Binder. "Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria." Molecular and Cellular Biology 21, no. 3 (February 1, 2001): 731–42. http://dx.doi.org/10.1128/mcb.21.3.731-742.2001.

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ABSTRACT To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, peaatp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts.

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Begelman, David, Bhavna Dixit, Caitlin Lewis, Mark Watson, Martin Brand, and Amutha Boominathan. "Successful Exogenous Expression of ATP8, a Mitochondrial Encoded Protein, From the Nucleus In Vivo." Innovation in Aging 5, Supplement_1 (December 1, 2021): 686. http://dx.doi.org/10.1093/geroni/igab046.2577.

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Abstract Replicative errors, inefficient repair, and proximity to reactive oxygen species production sites make the mitochondrial DNA (mtDNA) susceptible to damage with time. mtDNA mutations accumulate with age and accompany a progressive decline in organelle function. We lack molecular biology tools to manipulate mtDNA, thus we explore the possibility in vivo of utilizing allotopic expression, or the re-engineering mitochondrial genes and expressing them from the nucleus, as an approach to rescue defects arising from mtDNA mutations. This study uses a mouse model with a mutation in the mitochondrial ATP8 gene that encodes a protein subunit of the ATP synthase. We generated a transgenic mouse with an epitope-tagged recoded and mitochondrial-targeted ATP8 gene expressed from the nucleus. Our results show that the allotopically expressed ATP8 protein in the transgenic mice is robustly expressed across all tested tissues, successfully transported into the mitochondria, and incorporated into ATP synthase. We are currently evaluating if allotopic expression of ATP8 will functionally rescue the behavioral and bioenergetic defects in ATP8 mutant mice. Translating allotopic expression technology into a mammal and demonstrating systemic functional rescue will lend credence to utilizing allotopic expression as a gene therapy in humans to repair physiological consequences of mtDNA defects that may accumulate with age.

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Zhang, Shuguang, Brendon J. Monahan, Jan S. Tkacz, and Barry Scott. "Indole-Diterpene Gene Cluster from Aspergillus flavus." Applied and Environmental Microbiology 70, no. 11 (November 2004): 6875–83. http://dx.doi.org/10.1128/aem.70.11.6875-6883.2004.

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ABSTRACT Aflatrem is a potent tremorgenic mycotoxin produced by the soil fungus Aspergillus flavus and is a member of a large structurally diverse group of secondary metabolites known as indole-diterpenes. By using degenerate primers for conserved domains of fungal geranylgeranyl diphosphate synthases, we cloned two genes, atmG and ggsA (an apparent pseudogene), from A. flavus. Adjacent to atmG are two other genes, atmC and atmM. These three genes have 64 to 70% amino acid sequence similarity and conserved synteny with a cluster of orthologous genes, paxG, paxC, and paxM, from Penicillium paxilli which are required for indole-diterpene biosynthesis. atmG, atmC, and atmM are coordinately expressed, with transcript levels dramatically increasing at the onset of aflatrem biosynthesis. A genomic copy of atmM can complement a paxM deletion mutant of P. paxilli, demonstrating that atmM is a functional homolog of paxM. Thus, atmG, atmC, and atmM are necessary, but not sufficient, for aflatrem biosynthesis by A. flavus. This provides the first genetic evidence for the biosynthetic pathway of aflatrem in A. flavus.

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Wu, Jiang, Ying Kai Tong, and Li Tong Ban. "Separation of Casein Phosphopeptides (a Functional Food Material) by Aqueous Two-Phase Systems." Advanced Materials Research 554-556 (July 2012): 1511–14. http://dx.doi.org/10.4028/www.scientific.net/amr.554-556.1511.

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PEG 10000 / (NH4)2SO4 ATPS was applied to extract casein phosphopeptides. By studying on the partitioning behavior of CPPs in this system, it is concluded that the purification fold of CPPs could reach 7.09 when the system consisted of 20% PEG 10000 and 10% (NH4)2SO4.

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Jugler, Collin, Jussi Joensuu, and Qiang Chen. "Hydrophobin-Protein A Fusion Protein Produced in Plants Efficiently Purified an Anti-West Nile Virus Monoclonal Antibody from Plant Extracts via Aqueous Two-Phase Separation." International Journal of Molecular Sciences 21, no. 6 (March 20, 2020): 2140. http://dx.doi.org/10.3390/ijms21062140.

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The development of monoclonal antibodies (mAbs) has provided vast opportunities to treat a wide range of diseases from cancer to viral infections. While plant-based production of mAbs has effectively lowered the upstream cost of mAb production compared to mammalian cell cultures, further optimization of downstream processing, especially in extending the longevity of Protein A resin by an effective bulk separation step, will further reduce the overall prohibitive cost of mAb production. In this study, we explored the feasibility of using aqueous two-phase separation (ATPS) in capturing and separating plant-made mAbs from host proteins. Our results demonstrated that an anti-West Nile virus mAb (E16) was efficiently separated from most plant host proteins by a single ATPS step, comprising the mixing of plant extracts containing Hydrophobin-Protein A fusion protein (HPA) and E16 and the subsequent incubation with an inexpensive detergent. This simple ATPS step yielded a highly enriched E16 mAb preparation with a recovery rate comparable to that of Protein A chromatography. The ATPS-enriched E16 retained its structural integrity and was fully functional in binding its target antigen. Notably, HPA-based ATPS was also effective in enriching E16 from plant host proteins when both HPA and E16 were produced in the same leaves, supporting the potential of further streamlining the downstream purification process. Thus, ATPS based on plant-produced HPA in unpurified extract is a cost-effective yet efficient initial capture step for purifying plant-made mAbs, which may significantly impact the approach of mAb purification.

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Johnson, Eric, and Melis Anastasios. "Functional characterization of Chlamydomonas reinhardtii with alterations in the atpE gene." Photosynthesis Research 82, no. 2 (November 2004): 131–40. http://dx.doi.org/10.1007/s11120-004-6567-1.

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Lubośny, Marek, Aleksandra Przyłucka, Beata Śmietanka, Sophie Breton, and Artur Burzyński. "Actively transcribed and expressed atp8 gene in Mytilus edulis mussels." PeerJ 6 (June 8, 2018): e4897. http://dx.doi.org/10.7717/peerj.4897.

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Background Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial. Results Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis. Conclusion Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).

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Zeng, Xiaomei, Mario H. Barros, Theodore Shulman, and Alexander Tzagoloff. "ATP25, a New Nuclear Gene ofSaccharomyces cerevisiaeRequired for Expression and Assembly of the Atp9p Subunit of Mitochondrial ATPase." Molecular Biology of the Cell 19, no. 4 (April 2008): 1366–77. http://dx.doi.org/10.1091/mbc.e07-08-0746.

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We report a new nuclear gene, designated ATP25 (reading frame YMR098C on chromosome XIII), required for expression of Atp9p (subunit 9) of the Saccharomyces cerevisiae mitochondrial proton translocating ATPase. Mutations in ATP25 elicit a deficit of ATP9 mRNA and of its translation product, thereby preventing assembly of functional F0. Unlike Atp9p, the other mitochondrial gene products, including ATPase subunits Atp6p and Atp8p, are synthesized normally in atp25 mutants. Northern analysis of mitochondrial RNAs in an atp25 temperature-sensitive mutant confirmed that Atp25p is required for stability of the ATP9 mRNA. Atp25p is a mitochondrial inner membrane protein with a predicted mass of 70 kDa. The primary translation product of ATP25 is cleaved in vivo after residue 292 to yield a 35-kDa C-terminal polypeptide. The C-terminal half of Atp25p is sufficient to stabilize the ATP9 mRNA and restore synthesis of Atp9p. Growth on respiratory substrates, however, depends on both halves of Atp25p, indicating that the N-terminal half has another function, which we propose to be oligomerization of Atp9p into a proper size ring structure.

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Xie, Guo, Xinhong Hei, Sei Takahashi, and Hideo Nakamura. "A Strategy to Formalize Specification and Its Application to an Advanced Railway System." International Journal of Software Engineering and Knowledge Engineering 24, no. 03 (April 2014): 465–92. http://dx.doi.org/10.1142/s0218194014500181.

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This paper proposes a novel strategy for formally analyzing functional requirements specification (FRS) and applies it to the Automatic Train Protection and Block (ATPB) system, which is proposed to reconstruct conventional rail lines in Japan. Based on the FRS in natural language, firstly, dynamic state transitions are extracted to express the operational mechanisms and determine the system parameters. A complete model of the ATPB system is then established using Unified Modeling Language (UML) to express the system structure graphically and explicitly. After achieving a common understanding, a VDM++ model is established formally to redescribe the original FRS of the ATPB system which is written in natural language (i.e. Japanese). Following that, in order to ensure internal consistency of the specification, proof obligations of the VDM++ model are discharged. Furthermore, a comprehensive testing is implemented to ensure that the FRS meets actual requirements. Finally, the system is simulated strictly in accordance with the formal specification. Without any runtime errors, collisions or derailments, the results of the simulation demonstrate the high quality and safety of the specification.

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Hoffmann, Michaela, and Stefan Binder. "Functional Importance of Nucleotide Identities Within the Pea atp9 Mitochondrial Promoter Sequence." Journal of Molecular Biology 320, no. 5 (July 2002): 943–50. http://dx.doi.org/10.1016/s0022-2836(02)00552-1.

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Kenvin, Sebastian, Ruben Torregrosa-Muñumer, Marco Reidelbach, Jana Pennonen, Jeremi J. Turkia, Erika Rannila, Jouni Kvist, et al. "Threshold of heteroplasmic truncating MT-ATP6 mutation in reprogramming, Notch hyperactivation and motor neuron metabolism." Human Molecular Genetics 31, no. 6 (October 12, 2021): 958–74. http://dx.doi.org/10.1093/hmg/ddab299.

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Abstract Mutations in mitochondrial DNA encoded subunit of ATP synthase, MT-ATP6, are frequent causes of neurological mitochondrial diseases with a range of phenotypes from Leigh syndrome and NARP to ataxias and neuropathies. Here we investigated the functional consequences of an unusual heteroplasmic truncating mutation m.9154C>T in MT-ATP6, which caused peripheral neuropathy, ataxia and IgA nephropathy. ATP synthase not only generates cellular ATP, but its dimerization is required for mitochondrial cristae formation. Accordingly, the MT-ATP6 truncating mutation impaired the assembly of ATP synthase and disrupted cristae morphology, supporting our molecular dynamics simulations that predicted destabilized a/c subunit subcomplex. Next, we modeled the effects of the truncating mutation using patient-specific induced pluripotent stem cells. Unexpectedly, depending on mutation heteroplasmy level, the truncation showed multiple threshold effects in cellular reprogramming, neurogenesis and in metabolism of mature motor neurons (MN). Interestingly, MN differentiation beyond progenitor stage was impaired by Notch hyperactivation in the MT-ATP6 mutant, but not by rotenone-induced inhibition of mitochondrial respiration, suggesting that altered mitochondrial morphology contributed to Notch hyperactivation. Finally, we also identified a lower mutation threshold for a metabolic shift in mature MN, affecting lactate utilization, which may be relevant for understanding the mechanisms of mitochondrial involvement in peripheral motor neuropathies. These results establish a critical and disease-relevant role for ATP synthase in human cell fate decisions and neuronal metabolism.

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Bugiardini, Enrico, Emanuela Bottani, Silvia Marchet, Olivia V. Poole, Cristiane Beninca, Alejandro Horga, Cathy Woodward, et al. "Expanding the molecular and phenotypic spectrum of truncating MT-ATP6 mutations." Neurology Genetics 6, no. 1 (January 8, 2020): e381. http://dx.doi.org/10.1212/nxg.0000000000000381.

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ObjectiveTo describe the clinical and functional consequences of 1 novel and 1 previously reported truncating MT-ATP6 mutation.MethodsThree unrelated probands with mitochondrial encephalomyopathy harboring truncating MT-ATP6 mutations are reported. Transmitochondrial cybrid cell studies were used to confirm pathogenicity of 1 novel variant, and the effects of all 3 mutations on ATPase 6 and complex V structure and function were investigated.ResultsPatient 1 presented with adult-onset cerebellar ataxia, chronic kidney disease, and diabetes, whereas patient 2 had myoclonic epilepsy and cerebellar ataxia; both harbored the novel m.8782G>A; p.(Gly86*) mutation. Patient 3 exhibited cognitive decline, with posterior white matter abnormalities on brain MRI, and severely impaired renal function requiring transplantation. The m.8618dup; p.(Thr33Hisfs*32) mutation, previously associated with neurogenic muscle weakness, ataxia, and retinitis pigmentosa, was identified. All 3 probands demonstrated a broad range of heteroplasmy across different tissue types. Blue-native gel electrophoresis of cultured fibroblasts and skeletal muscle tissue confirmed multiple bands, suggestive of impaired complex V assembly. Microscale oxygraphy showed reduced basal respiration and adenosine triphosphate synthesis, while reactive oxygen species generation was increased. Transmitochondrial cybrid cell lines studies confirmed the deleterious effects of the novel m.8782 G>A; p.(Gly86*) mutation.ConclusionsWe expand the clinical and molecular spectrum of MT-ATP6-related mitochondrial disorders to include leukodystrophy, renal disease, and myoclonic epilepsy with cerebellar ataxia. Truncating MT-ATP6 mutations may exhibit highly variable mutant levels across different tissue types, an important consideration during genetic counseling.

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Jiang, Bin, Jiaxin Na, Lele Wang, Dongmei Li, Chunhong Liu, and Zhibiao Feng. "Reutilization of Food Waste: One-Step Extration, Purification and Characterization of Ovalbumin from Salted Egg White by Aqueous Two-Phase Flotation." Foods 8, no. 8 (July 25, 2019): 286. http://dx.doi.org/10.3390/foods8080286.

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For the purpose of reducing pollution and the reutilization of salted egg whites, which are byproducts of the manufacturing process of salted egg yolks and normally treated as waste, an aqueous two-phase flotation (ATPF) composed of polyethylene glycols (PEG 1000) and (NH4)2SO4 was applied to develop a simple, inexpensive and efficient process for the separation of ovalbumin (OVA) from salted egg whites. The effects of the concentration of PEG, the concentration of (NH4)2SO4, the flow rate and the flotation time on the flotation efficiency (Y) and purity (P) of OVA were investigated. A response surface method (RSM) experiment was carried out on the basis of a single-factor experiment. An efficient separation was achieved using ATPF containing 5 mL of 80% PEG 1000 (w/w), 28 mL of 28% (NH4)2SO4 (w/w), 35 mL/min of the flow rate and 30 min of the flotation time, while 2 mL of the salted egg white solution (salted eggs white (v): water (v) = 1:4) was loaded. Under the optimal conditions, Y and P of OVA could reach 82.15 ± 0.24% and 92.98 ± 0.68%, respectively. The purified OVA was characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), reverse phase high-performance liquid chromatography (RP-HPLC), liquid chromatography-nano electrospray ionisation mass spectrometry (Nano LC-ESI-MS/MS), ultraviolet spectrum (UV), fluorescence spectrum (FL) and fourier transform infrared spectroscopy (FT-IR). The results indicated that the purity of OVA obtained by ATPF was satisfactory and there was no obvious difference in the structure of the OVA separated by ATPF and the standard. The results of the functional properties revealed no significant differences between OVA obtained by ATPF and the standard in oil binding capacity, viscosity, emulsibility and foam capacity.

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Ganetzky, Rebecca, Elizabeth McCormick, Michael Bennett, Eiko Nakamaru Ogiso, Richard Rodenberg, and Marni J. Falk. "Known and novel ATP6 mutations: Delineation of the phenotypic spectrum and functional effects." Mitochondrion 24 (September 2015): S19. http://dx.doi.org/10.1016/j.mito.2015.07.057.

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Huo, Jianqiang, Dengjing Huang, Jing Zhang, Hua Fang, Bo Wang, Chunlei Wang, Zhanjun Ma, and Weibiao Liao. "Comparative Proteomic Analysis during the Involvement of Nitric Oxide in Hydrogen Gas-Improved Postharvest Freshness in Cut Lilies." International Journal of Molecular Sciences 19, no. 12 (December 9, 2018): 3955. http://dx.doi.org/10.3390/ijms19123955.

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Our previous studies suggested that both hydrogen gas (H2) and nitric oxide (NO) could enhance the postharvest freshness of cut flowers. However, the crosstalk of H2 and NO during that process is unknown. Here, cut lilies (Lilium “Manissa”) were used to investigate the relationship between H2 and NO and to identify differentially accumulated proteins during postharvest freshness. The results revealed that 1% hydrogen-rich water (HRW) and 150 μM sodium nitroprusside (SNP) significantly extended the vase life and quality, while NO inhibitors suppressed the positive effects of HRW. Proteomics analysis found 50 differentially accumulated proteins in lilies leaves which were classified into seven functional categories. Among them, ATP synthase CF1 alpha subunit (chloroplast) (AtpA) was up-regulated by HRW and down-regulated by NO inhibitor. The expression level of LlatpA gene was consistent with the result of proteomics analysis. The positive effect of HRW and SNP on ATP synthase activity was inhibited by NO inhibitor. Meanwhile, the physiological-level analysis of chlorophyll fluorescence and photosynthetic parameters also agreed with the expression of AtpA regulated by HRW and SNP. Altogether, our results suggested that NO might be involved in H2-improved freshness of cut lilies, and AtpA protein may play important roles during that process.

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Pugacheva, Margarita E., Galina A. Aleshkina, Leonid M. Bardenshteyn, and Nicolay I. Beglyankin. "Personalized approach to early diagnosis of acute schizophrenia: an observational comparative study." Medical Journal of the Russian Federation 28, no. 3 (August 29, 2022): 181–92. http://dx.doi.org/10.17816/medjrf109266.

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BACKGROUND: An acute schizophrenic episode often meets the diagnostic criteria for the ICD-10 category acute and transient psychotic disorders (ATPD, F23), which includes clinically similar conditions of diverse etiologies. The presence of schizophrenic negative symptoms in ATPD signifies their nosological affiliation and determines the therapeutic tactics. Early recognition of the schizophrenic etiology in the first episode of psychosis may contribute to the development of a personalized approach for the management of patients with acute psychotic disorders. AIM: To evaluate the relationship between the developmental characteristics of psychosis and identify the negative symptoms after its reduction in patients with ATPD with the symptoms of schizophrenia. MATERIALS AND METHODS: This observational single-center selective comparative study was conducted during 20182020. The clinical-psychopathological method was applied to examine patients hospitalized in a psychiatric hospital with ATPD presenting with the symptoms of schizophrenia (F23.1). In order to objectify the results of the study, the positive and negative syndrome scale was used. RESULTS: The study involved 60 patients (50 men, 10 women) aged 1846 years (mean age: 21.46.0 years). Depending on the presence of negative symptoms after the psychosis reduction at 4 weeks of therapy, the study sample was divided into two groups: 1) the group with negative symptoms (NS+; n=41); 2) the group without any negative symptoms (NS; n=19). Individuals presenting with negative symptoms were distinguished from those without it based on the more frequent presence of prodromal disorders, subpsychotic, and, particularly, mild negative disorders at the prodromal stage, prolonged development, and long-drawn course of psychosis. The likelihood of negative symptoms detection after the reduction of psychosis was associated with a family history of schizophrenia and other psychiatric disorders, low premorbid social adjustment, prodromal symptoms, and impaired functioning, as well as with a longer duration of psychotic symptoms and its slow development. CONCLUSION: The likelihood of negative symptoms after the reduction of ATPD with symptoms of schizophrenia was associated with hereditary and premorbid characteristics of patients, prodromal psychopathological and functional abnormalities, as well as the clinical and dynamic characteristics of psychosis. The data obtained from this study may contribute to the early recognition of schizophrenia-spectrum disorders and to the development of a personalized approach for the management of patients with ATPD.

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Wang, Jing, Mo Ju Cao, Guang Tang Pan, Yan Li Lu, and Ting Zhao Rong. "RNA editing of mitochondrial functional genes atp6 and cox2 in maize (Zea mays L.)." Mitochondrion 9, no. 5 (September 2009): 364–69. http://dx.doi.org/10.1016/j.mito.2009.07.005.

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Wu, Jiang, Li Tong Ban, and Yu Wang. "Separation of Curcumine (a Functional Food Colourant Material) from Rhizoma curcuma longae by Aqueous Two-Phase Systems." Applied Mechanics and Materials 217-219 (November 2012): 961–64. http://dx.doi.org/10.4028/www.scientific.net/amm.217-219.961.

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The objective of this paper was to separate curcumine from Rhizoma curcuma longae and aqueous two-phase extraction technology was employed to perform the study. Four types of PEG (400, 600, 2000 and 4000) and three types of salt ((NH4)2SO4, KH2PO4 and K2HPO4) were tested to form the aqueous two-phase systems. The results showed that the ATPS composed of PEG 400 and (NH4)2SO4 were the best. And the partition coefficient of curcumine could reach 21.79 when the concentration of PEG 400 and (NH4)2SO4 was 14.6% and 26% respectively.

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Sellami, Azza, Christian Wegener, and Jan A. Veenstra. "Functional significance of the copper transporter ATP7 in peptidergic neurons and endocrine cells inDrosophila melanogaster." FEBS Letters 586, no. 20 (August 16, 2012): 3633–38. http://dx.doi.org/10.1016/j.febslet.2012.08.009.

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Ding, Qiuju, Róża Kucharczyk, Weiwei Zhao, Alain Dautant, Shutian Xu, Katarzyna Niedzwiecka, Xin Su, et al. "Case Report: Identification of a Novel Variant (m.8909T>C) of Human Mitochondrial ATP6 Gene and Its Functional Consequences on Yeast ATP Synthase." Life 10, no. 9 (September 22, 2020): 215. http://dx.doi.org/10.3390/life10090215.

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With the advent of next generation sequencing, the list of mitochondrial DNA (mtDNA) mutations identified in patients rapidly and continuously expands. They are frequently found in a limited number of cases, sometimes a single individual (as with the case herein reported) and in heterogeneous genetic backgrounds (heteroplasmy), which makes it difficult to conclude about their pathogenicity and functional consequences. As an organism amenable to mitochondrial DNA manipulation, able to survive by fermentation to loss-of-function mtDNA mutations, and where heteroplasmy is unstable, Saccharomyces cerevisiae is an excellent model for investigating novel human mtDNA variants, in isolation and in a controlled genetic context. We herein report the identification of a novel variant in mitochondrial ATP6 gene, m.8909T>C. It was found in combination with the well-known pathogenic m.3243A>G mutation in mt-tRNALeu. We show that an equivalent of the m.8909T>C mutation compromises yeast adenosine tri-phosphate (ATP) synthase assembly/stability and reduces the rate of mitochondrial ATP synthesis by 20–30% compared to wild type yeast. Other previously reported ATP6 mutations with a well-established pathogenicity (like m.8993T>C and m.9176T>C) were shown to have similar effects on yeast ATP synthase. It can be inferred that alone the m.8909T>C variant has the potential to compromise human health.

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Jayasekera, Lakshika P., Ruwandi Ranasinghe, Kanishka S. Senathilake, Joanne T. Kotelawala, Kanishka de Silva, Priyanka H. Abeygunasekara, Renuka Goonesinghe, and Kamani H. Tennekoon. "Mitochondrial genome in sporadic breast cancer: A case control study and a proteomic analysis in a Sinhalese cohort from Sri Lanka." PLOS ONE 18, no. 2 (February 9, 2023): e0281620. http://dx.doi.org/10.1371/journal.pone.0281620.

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Breast cancer is the commonest malignancy in women and the majority occurs sporadically with no hereditary predisposition. However, sporadic breast cancer has been studied less intensively than the hereditary form and to date hardly any predictive biomarkers exist for the former. Furthermore, although mitochondrial DNA variants have been reported to be associated with breast cancer, findings have been inconsistent across populations. Thus we carried out a case control study on sporadic breast cancer patients and healthy controls of Sinhalese ethnicity (N = 60 matched pairs) in order to characterize coding region variants associated with the disease and to identify any potential biomarkers. Mitochondrial genome was fully sequenced in 30 pairs and selected regions were sequenced in the remaining 30 pairs. Several in-silico tools were used to assess functional significance of the variants observed. A number of variants were identified among the patients and the controls. Missense variants identified were either polymorphisms or rare variants. Their prevalence did not significantly differ between patients and the healthy controls (matched for age, body mass index and menopausal status). MT-CYB, MT-ATP6 and MT-ND2 genes showed a higher mutation rate. A higher proportion of pre-menopausal patients carried missense and pathogenic variants. Unique combinations of missense variants were seen within genes and these occurred mostly in MT-ATP6 and MT-CYB genes. Such unique combinations that occurred exclusively among the patients were common in obese patients. Mitochondrial DNA variants may have a role in breast carcinogenesis in obesity and pre-menopause. Molecular dynamic simulations suggested the mutants, G78S in MT-CO3 gene and T146A in MT-ATP6 gene are likely to be more stable than their wild type counterparts.

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Journal articles on the topic 'Functional ATPG'

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