scholarly journals A restriction site to differentiate Plasmodium and Haemoproteus infections in birds: on the inefficiency of general primers for detection of mixed infections

Parasitology ◽  
2009 ◽  
Vol 136 (7) ◽  
pp. 713-722 ◽  
Author(s):  
J. MARTÍNEZ ◽  
J. MARTÍNEZ-DE LA PUENTE ◽  
J. HERRERO ◽  
S. DEL CERRO ◽  
E. LOBATO ◽  
...  
Keyword(s):  
Restriction Site ◽  
General Rule ◽  
Dna Amplification ◽  
Additional Restriction ◽  
Mixed Infections ◽  
Specific Primers ◽  
Dna Analyses ◽  
Restriction Sites ◽  
Additional Restriction Site ◽  
Do So

SUMMARYAvian Plasmodium and Haemoproteus parasites are easily detected by DNA analyses of infected samples but only correctly assigned to each genus by sequencing and use of a phylogenetic approach. Here, we present a restriction site to differentiate between both parasite genera avoiding the use of those analyses. Alignments of 820 sequences currently listed in GenBank encoding a particular cytochrome B region of avian Plasmodium and Haemoproteus show a shared restriction site for both genera using the endonuclease Hpy CH4III. An additional restriction site is present in Plasmodium sequences that would initially allow differentiation of both genera by differential migration of digested products on gels. Overall 9 out of 326 sequences containing both potential restriction sites do not fit to the general rule. We used this differentiation of parasite genera based on Hpy CH4III restriction sites to evaluate the efficacy of 2 sets of general primers in detecting mixed infections. To do so, we used samples from hosts infected by parasites of both genera. The use of general primers was only able to detect 25% or less of the mixed infections. Therefore, parasite DNA amplification using general primers to determine the species composition of haemosporidian infections in individual hosts is not recommended. Specific primers for each species and study area should be designed until a new method can efficiently discriminate both parasites.

scholarly journals D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.

2011 ◽  
Vol 77 (18) ◽  
pp. 6722-6725 ◽  
Author(s):  
Sumit S. Dagar ◽  
Sanjay Kumar ◽  
Priti Mudgil ◽  
Rameshwar Singh ◽  
Anil K. Puniya
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
Large Subunit ◽  
Species Level ◽  
Additional Restriction ◽  
Lsu Rdna ◽  
Content Type ◽  
D2 Domain ◽  
Additional Restriction Site

ABSTRACTThis study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation ofOrpinomyces joyoniiandOrpinomyces intercalarisbased on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T inO. intercalariscreated an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation.

scholarly journals Bacterial Synergism—The Formation byB. typhosusorB. coli anaerogenesfrom Mannitol of an Intermediate Substance from which Morgan's Bacillus produces Gas

1932 ◽  
Vol 32 (3) ◽  
pp. 385-395
Author(s):  
J. Gibson Graham
Keyword(s):  
General Rule ◽  
Sodium Formate ◽  
General Term ◽  
Carbon Compounds ◽  
Combined Action ◽  
Bacterial Synergism ◽  
Micro Organisms ◽  
Bacterial Association ◽  
Do So ◽  
Intermediate Substance

In the operations of bacteria under natural conditions it is the general rule to find mixed cultures at work, the variability of the results depending upon many factors. Therefore it has been suggested by Holman (1928) that the general term “bacterial association” be used to cover such processes. When, however, the combined action of two or more micro-organisms effects changes which each by itself is incapable of achieving, the term “synergism” is applied. Synergism appears to be used now in a more restricted sense to describe a particular type of bacterial association, and has been defined by Fiallos (1925) as follows: “two bacilli neither of which causes the production of gas in certain compounds, may do so when artificially mixed together provided one of them is capable of producing acidity (never gas) in these carbon compounds, and the other though inert to these compounds (i.e. produces in them neither acid nor gas) is capable of producing gas from glucose.” In 1911 Penfold observed the production of gas from a glucose medium in whichB. typhosuswas growing along with a variant non-aerogenic strain ofB. coli communis, the latter having been derived from a typical gas-producing culture by selective growth on agar containing sodium monochloracetate. Although this organism had lost the power of gas-fermenting glucose it retained the power of gas-fermenting sodium formate. Castellani (1925, 1926 and 1927) states that he noted the phenomenon, which he calls “symbiotic,” in 1904 when investigating the fermentation reactions of bakers' yeast, which is not a pure culture but consists generally of two or more species of yeasts together with one or more types of Gram-negative bacilli.

Frequency and Tense Use in French

1998 ◽  
Vol 12 ◽  
pp. 43-60 ◽  
Author(s):  
Arie Molendijk ◽  
Henriette E. de Swart
Keyword(s):  
General Rule ◽  
Concrete Situation ◽  
Dependent Frequency ◽  
Temporal Relationships ◽  
The Absolute ◽  
Do So

Abstract. This paper deals wilh the use of Ihe passé simple and the imparfait of French in frequentative sentences. It is argued that frequency implies sentence-internal quantification, meaning that frequentative sentences report just one (complex) eventuality. This claim is related to the fact that, as far as establishing temporal relationships between eventualities is concerned, sentences containing frequency adverbs behave like sentences that don't imply quantification at all. So they may establish all kinds of temporal relationships between eventualities. Given the claims put forward in this paper about the temporal meaning of the passe* simple and the imparfait (Molendijk 1990), it naturally follows that, as a general rule, frequency adverbs combine with both tenses. But they do not always do so under exactly the same circumstances. In this regard, a distinction can be made between dependent frequency adverbs {tout le temps 'all the time' etc.), which imply reference to a contextually determinable concrete situation, and independent ones (toujours 'always', etc.), which may be used without any reference to such a situation. This distinction helps us to understand, for instance, why dependent frequency adverbs do not easily combine with the 'absolute' (non-narrative) passe simple, whereas they do combine with the imparfait and the 'narrative' passé simple.

scholarly journals The Child Justice Act: Procedural Sentencing Issues

2017 ◽  
Vol 16 (1) ◽  
pp. 320
Author(s):  
Stephan S Terblanche
Keyword(s):  
General Rule ◽  
Status Quo ◽  
Probation Officers ◽  
Care Centre ◽  
Older Children ◽  
Trial Courts ◽  
Victim Impact Statement ◽  
The Status ◽  
Do So

In this contribution a number of procedural issues related to the sentencing of child offenders and emanating from the Child Justice Act 75 of 2008 are considered in some detail. As a general rule, the Act requires pre-sentence reports to be obtained from probation officers before sentencing any child offender, with only a limited number of exceptions. The article argues that the peremptory nature of the Act means that a probation report is always required, even if reports by other experts are also available. The exceptions are limited to instances other than those where the child offender is sentenced to any form of imprisonment or to residence in a care centre. The article addresses the question of whether or not the reference to imprisonment includes alternative imprisonment which is imposed only as an alternative to a fine. It suggests that alternative imprisonment should, generally, not be imposed on child offenders. When an exception is not prevented because of the sentence, a pre-sentence report may be dispensed with only when the offence is a schedule-1 offence (the least serious class of offences) or when obtaining a report would prejudice the child. It is argued that these exceptions are likely to occur rather rarely. A final aspect of the Act’s provisions on pre-sentence reports is the requirement that reasons be given for a departure from the recommendations in a pre-sentence report. This requirement merely confirms the status quo. The Act permits the prosecutor to provide the court with a victim impact statement. Such a statement is defined in the Act. It is a sworn statement by a victim or someone authorised by the victim explaining the consequences to the victim of the commission of the crime. The article also addresses the issue of whether or not the child justice court might mero motu obtain a victim impact statement when the prosecution does not do so. Finally, the article addresses appeals against and reviews of the trial courts’ sentences. It notes that appeal by the child offender is made somewhat easier, as some child offenders need not obtain leave to appeal. These include children under the age of 16, or older children sentenced to imprisonment. Again, the meaning of “imprisonment” is at least somewhat ambiguous. The provisions on automatic review have attracted considerable judicial attention already. The majority of these judgments confirmed the apparently clear wording of the Act, in terms of which the cases of all child offenders under the age of 16 should be reviewed regardless of whether they were legally represented or of the sentence imposed. In the case of child offenders aged 16 or 17, only custodial sentences are reviewable. The judgments which found this to be an incorrect interpretation are dealt with in some detail, with the conclusion that they were incorrectly decided.

scholarly journals Naturally occurring variation in the restriction map of the amy region of Drosophila melanogaster.

Genetics ◽  
1988 ◽  
Vol 119 (3) ◽  
pp. 619-629
Author(s):  
C H Langley ◽  
A E Shrimpton ◽  
T Yamazaki ◽  
N Miyashita ◽  
Y Matsuo ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Restriction Site ◽  
Natural Populations ◽  
Alpha Amylase ◽  
Low Frequencies ◽  
Linkage Disequilibria ◽  
Restriction Sites ◽  
Site Variation ◽  
Transcriptional Units ◽  
Polymorphic Restriction

Abstract The restriction maps of 85 alleles of the Amy region of Drosophila melanogaster from natural populations were surveyed. A subset of these were also scored for allozyme phenotype and adult enzyme activity of alpha-amylase. Large insertions were found in 12% of the alleles in a 15-kb region surrounding the two transcriptional units of the duplicated Amy locus. The low frequencies at which each of these large insertions were found are consistent with earlier reports of variation in other loci. Four small deletions were found in the region 5' to the Amy genes. Each was also rare in the population. Restriction site variation provided an estimate of per nucleotide heterozygosity of 0.006. Several statistically significant linkage disequilibria were observed between four polymorphic restriction sites and the allozymes. Adult alpha-amylase activity was correlated with the allozymes and with the polymorphism at one restriction site close to the transcriptional units.

scholarly journals Evidence for random distribution of sequence variants in Tenebrio molitor satellite DNA

1992 ◽  
Vol 60 (1) ◽  
pp. 7-13 ◽  
Author(s):  
Miroslav Plohl ◽  
Branko Borˇstnik ◽  
Vlatka Lucijanić-Justić ◽  
ÐurÐica Ugarković
Keyword(s):  
Satellite Dna ◽  
Theoretical Calculations ◽  
Restriction Enzymes ◽  
Tenebrio Molitor ◽  
High Rate ◽  
Additional Restriction ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Sequential Organization ◽  
Restriction Sites

SummaryTenebrio molitor satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus satellite sequence, producing additional restriction sites. The ladder of satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the satellite. A defined higher order repeating structure, indicating the existence of satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50 % of the monomers, while others are very rare (0-1 % of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor satellite DNA is always random. Monomer variants are randomly distributed in the total satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.

A simplified procedure for cDNA and genomic library construction using nonpalindromic oligonucleotide adaptors

1989 ◽  
Vol 67 (4-5) ◽  
pp. 205-209 ◽  
Author(s):  
Cynthia R. D'Souza ◽  
Ken V. Deugau ◽  
John H. Spencer
Keyword(s):  
Genomic Dna ◽  
Restriction Site ◽  
Genomic Library ◽  
Restriction Endonuclease Site ◽  
Dna Libraries ◽  
Target Dna ◽  
Restriction Sites ◽  
Enzyme Cleavage ◽  
Simplified Procedure ◽  
Genomic Cdna

The properties and characteristics of oligonucleotide adaptors for use in a simplified procedure for the construction of cDNA and genomic DNA libraries are described. The adaptors are suitable for joining to blunt ended cDNA or sheared genomic DNA, and then to the cohesive ends of restriction sites in vectors. Each adaptor consists of two oligonucleotides with complementary but nonpalindromic sequences that include an internal restriction site, a 5′ phosphorylated blunt end, and an overlapping or staggered 5′ hydroxylated end corresponding to a restriction endonuclease site in a vector of choice. Ligation of the blunt end to high molecular weight target DNA proceeds efficiently and there is no tandem concatenation of the adaptor. Insertion into the appropriate vector only requires ligation of the cohesive ends. There is no requirement for methylation, restriction enzyme cleavage, G-C tailing, or denaturation after ligation of the adaptor to the target DNA, all characteristics of other procedures.Key words: library, genomic, cDNA, oligonucleotides, adaptors.

scholarly journals Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

2015 ◽  
Author(s):  
Tomasz Suchan ◽  
Camille Pitteloud ◽  
Nadezhda S. Gerasimova ◽  
Anna Kostikova ◽  
Sarah Schmid ◽  
...  
Keyword(s):  
Restriction Site ◽  
Degraded Dna ◽  
Model Organisms ◽  
Butterfly Species ◽  
Large Set ◽  
Grasshopper Species ◽  
Size Selection ◽  
Restriction Sites ◽  
Museum Samples ◽  
Orthologous Loci

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.

scholarly journals EVOLUTIONARY CHANGE OF RESTRICTION CLEAVAGE SITES AND PHYLOGENETIC INFERENCE

Genetics ◽  
1986 ◽  
Vol 113 (1) ◽  
pp. 187-213
Author(s):  
Wen-Hsiung Li
Keyword(s):  
Nucleotide Substitution ◽  
Restriction Site ◽  
Evolutionary Change ◽  
Cleavage Sites ◽  
Restriction Sites ◽  
Unequal Rates ◽  
Mathematical Formulas ◽  
Recent Species ◽  
Restriction Cleavage ◽  
Evolutionary Lineages

ABSTRACT Mathematical formulas are developed for the evolutionary change of restriction cleavage sites in a DNA sequence, allowing unequal rates between transitional and transversional types of nucleotide substitution. Formulas are also developed for the probability of having a particular pattern of site changes among evolutionary lineages, such as parallel gains or losses of sites, and for inferring the presence or absence of a restriction site in an ancestral sequence from data on the present-day sequences. The unordered compatibility method is proposed for inferring the phylogenetic relationships among relatively closely related organisms, treating restriction sites as cladistic characters. Formulas are derived for the probability (P  +) of obtaining the correct network for a given number (N) of informative sites for the cases of four and five species. These formulas are applied to evaluate the performance of the method and to estimate the N value required for P  + to be 95% or larger. The method performs well when the branches between ancestral nodes and the branches leading to the two most recent species are more or less equal in length, but performs poorly when the latter two branches are considerably longer than the former.

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