MISMATCH: A basis for semi-automatic functional mixed-signal test-pattern generation

This paper describes a tool which assists the designer in the rapid generation of functional tests for mixed-signal circuits down to the actual test-signals for the tester. The tool is based on manipulating design data, making use of macro-based test libraries and tester resources provided by the test engineer, and computer-based interaction with the designe

A low-speed BIST framework for high-performance circuit testing

Testing of high performance integrated circuits is becoming increasingly a challenging task owing to high clock frequencies. Often testers are not able to test such devices due to their limited high frequency capabilities. In this article we outline a design-for-test methodology such that high performance devices can be tested on relatively low performance testers. In addition, a BIST framework is discussed based on this methodology. Various implementation aspects of this technique are also addresse

Bridging the Testing Speed Gap: Design for Delay Testability

The economic testing of high-speed digital ICs is becoming increasingly problematic. Even advanced, expensive testers are not always capable of testing these ICs because of their high-speed limitations. This paper focuses on a design for delay testability technique such that high-speed ICs can be tested using inexpensive, low-speed ATE. Also extensions for possible full BIST of delay faults are addresse

L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes

Transcription of transposable elements interspersed in the genome is controlled by complex interactions between their regulatory elements and host factors. However, the same regulatory elements may be occasionally used for the transcription of host genes. One such example is the human L1 retrotransposon, which contains an antisense promoter (ASP) driving transcription into adjacent genes yielding chimeric transcripts. We have characterized 49 chimeric mRNAs corresponding to sense and antisense strands of human genes. Here we show that L1 ASP is capable of functioning as an alternative promoter, giving rise to a chimeric transcript whose coding region is identical to the ORF of mRNA of the following genes: KIAA1797, CLCN5, and SLCO1A2. Furthermore, in these cases the activity of L1 ASP is tissue-specific and may expand the expression pattern of the respective gene. The activity of L1 ASP is tissue-specific also in cases where L1 ASP produces antisense RNAs complementary to COL11A1 and BOLL mRNAs. Simultaneous assessment of the activity of L1 ASPs in multiple loci revealed the presence of L1 ASP-derived transcripts in all human tissues examined. We also demonstrate that L1 ASP can act as a promoter in vivo and predict that it has a heterogeneous transcription initiation site. Our data suggest that L1 ASP-driven transcription may increase the transcriptional flexibility of several human genes

Patterns of exotic plant species in the Netherlands: a macroecological perspective

In dit proefschrift heb is onderzocht wat mogelijkheden zijn om het invasief potentieel van geïntroduceerde plantensoorten en de invasibiliteit van plantengemeenschappen in Nederland te voorspellen. Soorten zijn gebruikt die hier al geïntroduceerd zijn, omdat van deze hun invasief succes bekend is. Om hun invasiviteit te kwantificeren is informatie gebruikt over de regionale en lokale verspreiding. De unieke beschikbaarheid van deze datasets voor plantensoorten in Nederland bieden nieuwe kansen, die mogelijk helpen de voorspelbaarheid van invasiviteit te verhogen, uit te leggen hoe invasiviteit van een soort kan veranderen in de tijd en hoe de samenstelling van de plantengemeenschap kan bepalen welke geïntroduceerde soorten zich kunnen vestigen

A Low Speed BIST Framework for High Speed Circuit Testing

Testing of high performance integrated circuits is becoming increasingly a challenging task owing to high clock frequencies. Often testers are not able to test such devices due to their limited high frequency capabilities. In this article we outline a design-for-test methodology such that high performance devices can be tested on relatively low performance testers. In addition, a BIST framework is discussed based on this methodology. Various implementation aspects of this technique are also addresse

Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA

<p>Abstract</p> <p>Background</p> <p>In a traditional electrophoresis mobility shift assay (EMSA) a ³²P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel electrophoresis (PAGE) in nondenaturing conditions. An extension of this method uses the large population of fragments derived from long genomic regions (approximately 600 kb) for the identification of fragments containing protein binding regions. With this method, genomic DNA is fragmented by restriction enzymes, fragments are amplified by PCR, radiolabeled, incubated with nuclear proteins and the resulting DNA-protein complexes are separated by two-dimensional PAGE. Shifted DNA fragments containing protein binding sites are identified by using additional procedures, i. e. gel elution, PCR amplification, cloning and sequencing. Although the method allows simultaneous analysis of a large population of fragments, it is relatively laborious and can be used to detect only high affinity protein binding sites. Here we propose an alternative and straightforward strategy which is based on a combination of native and denaturing PAGE. This strategy allows the identification of DNA fragments containing low as well as high affinity protein binding regions, derived from genomic DNA (<10 kb) of known sequence.</p> <p>Results</p> <p>We have combined an EMSA-based selection step with subsequent denaturing PAGE for the localization of protein binding regions in long (up to10 kb) fragments of genomic DNA. Our strategy consists of the following steps: digestion of genomic DNA with a 4-cutter restriction enzyme (<it>Alu</it>I, <it>Bsu</it>RI, <it>Tru</it>I, etc), separation of low and high molecular weight fractions of resultant DNA fragments, ³²P-labeling with Klenow polymerase, traditional EMSA, gel elution and identification of the shifted bands (or smear) by denaturing PAGE. The identification of DNA fragments containing protein binding sites is carried out by running the gel-eluted fragments alongside with the full "spectrum" of initial restriction fragments of known size. Here the strategy is used for the identification of protein-binding regions in the 5' region of the rat p75 neurotrophin receptor (<it>p75NTR</it>) gene.</p> <p>Conclusion</p> <p>The developed strategy is based on a combination of traditional EMSA and denaturing PAGE for the identification of protein binding regions in long fragments of genomic DNA. The identification is straightforward and can be applied to shifted bands corresponding to stable DNA-protein complexes as well as unstable complexes, which undergo dissociation during electrophoresis.</p

A potential role of alternative splicing in the regulation of the transcriptional activity of human GLI2 in gonadal tissues

BACKGROUND: Mammalian Gli proteins are important transcription factors involved in the regulation of Sonic hedgehog signal transduction pathway. Association of Gli2 with mammalian development and human disease led us to study the structure and expression of the human GLI2. RESULTS: We show that the region encoding GLI2 repressor domain is subject to alternative splicing in the gonadal tissues and different cell lines. Two major alternatively spliced forms of GLI2 mRNA arise from skipping exon 3 (GLI2Δ3) or exons 4 and 5 (GLI2Δ4–5). Both forms contain premature translational stop codons in the GLI2 open reading frame (ORF) starting from exon 2. Translation of GLI2Δ3 and GLI2Δ4–5 in vitro, initiated from downstream AUG codons, produced N-terminally truncated proteins. In Gli-dependent transactivation assay, expression of GLI2Δ3 induced activation of the reporter gene similar to that of the full-length construct (GLI2fl) containing complete ORF. However, expression of the GLI2Δ4–5 resulted in about 10-fold increase in activation, suggesting that deletion of the major part of repressor domain was responsible for the enhanced activation of GLI2 protein. CONCLUSION: Our data suggest that in addition to proteolytic processing, alternative splicing may be another important regulatory mechanism for the modulation of repressor and activator properties of GLI2 protein

De ontwikkeling van een informatiesysteem voor invasieve plantensoorten

De laatste decennia kent de Nederlandse flora een sterke toename van exoten. Soorten die door een sterke uitbreiding of verdichting van hun areaal overlast veroorzaken, worden invasieve soorten genoemd. De overlast van invasieve soorten (vaak kortweg invasieven genoemd) kan bestaan uit economische schade en gezondheids- en/of veiligheidsproblemen. Het Ministerie van Landbouw, Natuur en Voedselkwaliteit heeft daarom het Uitvoeringsconsortium Invasieve Plantensoorten een FES‑subsidie verleend om in vier jaar tijd een informatiesysteem over potentieel invasieve exotische plantensoorten op te zetten. Doel is informatie aan te leveren op basis waarvan ingeschat kan worden hoe groot de kans is dat exotische soorten zich bij introductie in Nederland invasief zullen gaan gedragen. Daarnaast is het doel hulp te bieden bij het herkennen van zulke soorten als ze worden geïmporteerd. Het informatiesysteem is ondergebracht in Q-bank

Pharmacological Inhibition of Epac1 Averts Ferroptosis Cell Death by Preserving Mitochondrial Integrity

Exchange proteins directly activated by cAMP (Epac) proteins are implicated in a wide range of cellular functions including oxidative stress and cell survival. Mitochondrial-dependent oxidative stress has been associated with progressive neuronal death underlying the pathology of many neurodegenerative diseases. The role of Epac modulation in neuronal cells in relation to cell survival and death, as well as its potential effect on mitochondrial function, is not well established. In immortalized hippocampal (HT-22) neuronal cells, we examined mitochondria function in the presence of various Epac pharmacological modulators in response to oxidative stress due to ferroptosis. Our study revealed that selective pharmacological modulation of Epac1 or Epac2 isoforms, exerted differential effects in erastin-induced ferroptosis conditions in HT-22 cells. Epac1 inhibition prevented cell death and loss of mitochondrial integrity induced by ferroptosis, while Epac2 inhibition had limited effects. Our data suggest Epac1 as a plausible therapeutic target for preventing ferroptosis cell death associated with neurodegenerative diseases