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Evaluation of low trace DNA recovery techniques from ridged surfaces

Evaluation of low trace DNA recovery techniques from ridged surfaces

Although there is literature supporting the use of flocked swabs [1], these are limited to post-coital vaginal swabs and therefore do not necessarily relate to touch DNA on ridged surfaces. There is also a study by Hansson et al investigating DNA recovery techniques from clothing [6] which also considered flocked swabs as well as tape lifts. This study also indicated that tape lifts recovered more DNA from clothing than flocked swabs; thus supporting the findings of this study, albeit on a different surface type.

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Efficacy of Bisulfite Modification and DNA Recovery Using Commercial Kits from Samples of Genomic and Circulating DNA

Efficacy of Bisulfite Modification and DNA Recovery Using Commercial Kits from Samples of Genomic and Circulating DNA

In sum, EZ DNA Methylation-Gold Kit from Zymo Research provided the highest yield of DNA after bisulfite treatment and isolation; the mean yield of DNA was no less than 86%. In addition, the efficacy of DNA recovery after treatment with Zymo Research kit does not depend on starting DNA concentration. This is in contrast to other kits tested, which provided no more than 20% yield for high DNA concentrations and only 2.7–5.8% for low DNA concentrations. A low concentration of cirDNA in the blood and, correspondingly, low amounts of these DNAs available for analytical procedures along with their fragmentation as well as size and compositional diversity of DNA fragments demand the most efficient protocol of DNA bisulfite treatment. A high recovery rate of DNA after treatment with EZ DNA Methylation-Gold Kit demonstrates that this kit is the most appropriate for cirDNA treatment. Thus, the treatment of cirDNA from both healthy donors and cancer patients with EZ DNA Methylation-Gold Kit provides almost quantitative DNA recovery after treatment and confirms that this protocol can be recommended for treatment of cirDNA.
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Reduced PCR Sensitivity Due to Impaired DNA Recovery with the MagNA Pure LC Total Nucleic Acid Isolation Kit

Reduced PCR Sensitivity Due to Impaired DNA Recovery with the MagNA Pure LC Total Nucleic Acid Isolation Kit

We have evaluated the performance of M extraction as an automated NA extraction system, aiming to replace the man- ual Si extraction procedure that we currently use for several applications. DNA recovery experiments with HindIII-di- gested phage lambda DNA and HaeIII-digested ␾ X174 DNA showed substantially lower DNA yields for M extraction com- pared to Si extraction, with, on average, 6.6-fold lower recov- eries for M extraction. A major problem identified with M extraction was the retrieval of DNA from the magnetic glass particles, where up to 60% of the DNA could not be retrieved. PCR signals of spiked PCR control DNAs for EBV and VZV were also between 1.9- and 14.2-fold lower after M extraction compared to Si extraction, also suggesting impaired DNA re- covery. This resulted in a 5- to 10-fold reduction in PCR sensitivity when spiked CMV strain AD 169 was extracted from whole blood by M extraction. Furthermore, it also resulted in false-negative results with 10 (4 EBV, 6 CMV) of the 39 clin- ical whole blood specimens tested. For manual Si extraction, high yields were observed with minimal loss of DNA during the procedure, which is in accordance with previous studies (2, 3, 5, 6, 8).
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Exploring the Potential of a Wet-Vacuum Collection System for DNA Recovery

Exploring the Potential of a Wet-Vacuum Collection System for DNA Recovery

Briefly, with the vacuum switch in the off position, the sampling handset of the wet-vacuum system was placed perpendicular to the surface. The vacuum switch was turned on and the buffer switch located on the handset was pushed to the on position. By steadily holding the handset on the surface, the handset was continuously repositioned over the stain such that the entire stain made contact with the buffer. A volume of 100 mL of buffer was used to collect each sample. Once the sample was collected, the buffer switch was turned off while the vacuum remained on and the handset continued to be in contact with the surface for an additional 5 seconds. The vacuum was then switched off and the collection bottle was detached for processing. Following this, the solution in the collection bottles was filtered through Millipore- Durapore 0.45 μm membrane filters. The filter paper was allowed to dry and was then cut into ¼ and ¾ slices for presumptive and DNA processing, respectively. If it is assumed that the cellular material is equally dispersed in the M-Vac collection buffer, and the filtering occurs through the center of the apparatus, then cutting the filter into ¼ and ¾ slices represents 25% and 75% of the available biological material. A negative glassware control was collected using a sterile swab, moistened with DI H 2 O. This
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DNA recovery from archived RDTs for genetic characterization of Plasmodium falciparum in a routine setting in Lambaréné, Gabon

DNA recovery from archived RDTs for genetic characterization of Plasmodium falciparum in a routine setting in Lambaréné, Gabon

Reliable, appropriate and timely diagnosis of febrile malaria patients is crucial, especially those caused by Plasmodium falciparum. This is achieved by micros- copy of thick blood smears and/or using a malaria rapid diagnostic test (RDT) [2]. In addition, nucleic acid test- ing (NAT) is used to detect low-density Plasmodium infections in epidemiological studies aimed at surveil- lance of malaria control and elimination. The DNA tem- plate for NAT is usually recovered from anti-coagulant (EDTA)-treated blood or blood spotted on filter paper [3] and sometimes from thick blood smears [4]. Venous fresh blood sampling requires special storage condi- tions and training in venipuncture. Additionally, the use of venous blood samples leads to somewhat lower diag- nostic sensitivity compared to capillary blood [5]. Capil- lary sampling is usually used for thick blood smears and sampling for RDTs or filter paper. Quality of DNA recov- ered from thick blood smears is low compared to filter paper and fresh blood [6] and the use of filter paper has to be prospectively planned, since it is not part of rou- tine diagnostics. RDTs support rational and timely use of anti-malarial drugs in field settings, particularly if reliable microscopy is not available [7, 8]. The ease of use, low cost, and performance of RDTs has led to an increase in sales of these supplies in Africa from 240 million in 2015 to 269 million in 2016 [8]. Furthermore, successful ampli- fication of DNA recovered from RDTs was observed [9–12] and the PCR detection rate in DNA extracted from RDTs is similar to that from filter paper [13]. Con- sequently, RDTs potentially represent an ideal source for large-scale retrospective analyses of parasite populations.
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Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures

Extrapolating our results on fresh teeth to more typical forensic cases involving aged and degraded skeletal remains may not be justified without further research. However, in cases of short postmortem intervals, where human remains are well preserved or in diseased teeth or those from elderly individuals (where pulp is absent or reduced), targeted sampling of cementum as an alternative for DNA analysis and identification offers a number of key advantages. Cementum is readily accessible and easily sampled using manual sampling tools, eliminating the need for specialist equipment to cut, drill and/or grind the teeth thus reducing cross-contamination risks and expense. The DNA extraction process is also simplified and is successful from small sample sizes (15–50 mg) using small volume extraction protocols with the potential for much higher throughput. Cementum contains less mineral than enamel, dentine or even bone, decreasing dependence on EDTA demineralisation steps. In contrast to dentine, DNA recovery from cementum is not adversely affected by dental disease nor age of the individual.
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Recovery identity and wellbeing: is it better to be 'recovered' or 'in recovery'?

Recovery identity and wellbeing: is it better to be 'recovered' or 'in recovery'?

A significant challenge in attempting to define recovery relates to the underlying philosophical assumptions about recovery that are related to specific models of change. Two in particular will be contrasted in the analysis presented below, and those relate to the differentiation between the model of recovery outlined in therapeutic communities ('TC') approaches (De Leon, 2000) and the model outlined in 12-step mutual aid writings (Kelly, 2016). Although not considered in the consensus group definitions, recovery differs fundamentally between these two approaches, in that within the TC model recovery is a state that has been achieved (i.e. 'I am recovered' or 'I am an ex- addict'). In contrast, within the 12-step model, recovery is a never-ending journey of growth and development where the individual continues to be 'in recovery' and if they consider themselves to be 'recovered' then they are at heightened risk of relapse. According to Denzin (1987), people attending AA members know that they will have the 'disease' of addiction until they die. Smith’s (2007) study of AA’s social world suggests that AA members frame their condition as a ‘sickness’ to be treated with aid of a sponsor and participation with AA’s 12 Step.
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DNA methylation and DNA methyltransferases

DNA methylation and DNA methyltransferases

model, the first wave of demethylation occurs during the migration of proliferating primordial germ cells, with remethylation occurring in postmigratory germ cells; the second wave of demethylation takes place in cleav- age stage embryos and results in a minimum in DNA methylation at the blastocyst stage. As shown in Fig.  2, this standard double-dip model obscures the methyla- tion dynamics of the small fraction of the genome shown in Fig.  1 where methylation is likely to exert regulatory effects. First, the large majority of CpG island promot- ers are not subject to these waves of methylation and demethylation because they are unmethylated at all stages. Second, the methylation status of alleles at dif- ferentially methylated regions (DMRs) of imprinting control regions (ICRs) changes at different developmen- tal stages: they are demethylated in primordial germ cells and remethylated in cohorts of growing oocytes shortly before ovulation [11] and in the entire popula- tion of prospermatogonia around the time of birth [12]. The sex-specific methylation at ICRs/DMRs escapes the demethylation that occurs in cleavage stage embryos. Third, the small population of young, CpG-rich trans- posons largely escapes demethylation both in primordial germ cells [13] and in the early embryo [14]. The types of sequences that undergo the double wave of demeth- ylation and remethylation are largely composed of old and inactive transposon remnants, satellite and other repeated DNA, and the unannotated and rapidly diverg- ing fraction of the genome that shows little evidence of biological function. Figure 2 shows that the dynamics of demethylation and remethylation during development are more complex than depicted in the double-dip model and that sequences whose methylation status is of biolog- ical importance do not conform to this model.
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Measuring Spiritual Recovery: The Spiritual Recovery Scale

Measuring Spiritual Recovery: The Spiritual Recovery Scale

Dr Bohan noted when recovering sex addicts checked into group they gave as a spiritual check in, information about their prayer life and as to whether they had attended a religious meeting since their last group. He saw that information as important more like an objectives but not the spiritual goals. The next slide has the first Spiritual Recovery Scale showing contrasting items, spiritual deficiency items on the left and the spiritual recovery goals on the right.

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Uncovering recovery: the resistible rise of recovery and resilience

Uncovering recovery: the resistible rise of recovery and resilience

The individualized personal nature of recovery is a central theme across another UK policy document, this time from Rethink, a leading UK mental health membership charity. The document is entitled 100 ways to support Recovery (Slade, 2009). Like the cross government strategy this document draws from the work of Anthony to provide a framework for recovery but adds a distinction between ‘personal recovery’ (seen as within the domain of the ‘expertise of people with lived experience of mental illness’) and ‘clinical recovery’ (seen as within the domain of the ‘expertise of mental health professionals’). Clinical recovery is concerned with the eradication of symptoms, the restoration of ‘social functioning’ and other ways of ‘getting back to normal’, (p.4). This distinction functions to effectively locate ‘personal recovery’ as an adjunct to clinical recovery, and this complementarity avoids recovery being seen as inherently contested.
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Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR

Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR

Quantitative PCR methods. Two TaqMan-based PCR assays were used to measure fungal DNA using a GeneAmp 7900 sequence detection system (Ap- plied Biosystems, Foster City, CA) with primers that target highly conserved regions of the fungal 18S rRNA gene and 5 ⬘ nuclease probes complementary to Aspergillus species or Candida species 18S rRNA genes. For the Aspergillus fumigatus assay, we used primers Fun-18S-995F (5 ⬘ -CGATYAGATACCGTYG TAGTC-3⬘), Fun-18S-1217R (5⬘TGTCTGGACCTGGTGAGTTT-3⬘), and a 6-carboxyfluorescein (FAM)-labeled probe with a Black Hole quencher (BHQ1) (5⬘-FAM-TTTCTATGATGACCCGCTCGGCA-BHQ1-3⬘). For the Candida albicans qPCR assay, we used primers Fun-18S-1313F (5 ⬘ -SCGATAACGAAC GAGACCT-3⬘) and Fun-18S-1467R (5⬘-TAGCGCGCTGCGGCCCAGA-3⬘) with a VIC (Applied Biosystems)-labeled probe and a 6-carboxytetramethylrho- damine (TAMRA) quencher (5⬘-VIC-CTAAATAGTGSTGCTAGCWTTTGC- TAMRA-3 ⬘ ). The concentration of each primer was 200 nM, and the concen- tration of each probe was 100 nM. We used Universal master mix (Applied Biosystems) for all qPCR reactions and ran each sample in a 50- ␮ l volume consisting of 5 ␮l of target DNA and 45 ␮l of master mix with primers and probe. PCR conditions included a 2-minute incubation at 50°C to inactivate previous amplicons with uracil-DNA glycosylase, followed by a 10-minute incubation at 95°C to activate the Taq Gold polymerase. Forty-five cycles of PCR, consisting of 15 seconds at 95°C, 30 seconds at 55°C, and 30 seconds at 65°C, were performed. All qPCR assays contained 4 no-template control samples (negative controls) and 12 samples consisting of Aspergillus fumigatus or Candida albicans genomic DNA (as appropriate) added to reactions in duplicate to produce standards of 1,000 pg, 100 pg, 10 pg, 1 pg, 100 fg, and 20 fg of fungal genomic DNA. The threshold cycle values from the genomic DNA standards were used to create a standard curve to assess the amount of fungal DNA in samples subjected to the various DNA extraction methods. All samples from extraction replicates were run in duplicate. Amplification controls were performed on DNA extracted from each method; 5 ␮ l of extracted DNA was combined with 1 ␮ l of 1,000-pg fungal genomic DNA standard, and qPCR was performed on this mixture. If PCR inhibitors are present in the extracted DNA, the threshold cycle for that sample shifts to a higher cycle number compared to the 1,000-pg standard without exogenous sample DNA. Digest controls consisted of sterile UV-irradiated water processed through each of the DNA extraction methods and then analyzed by qPCR.
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A meta recovery framework: positioning the ‘New Recovery’ movement and other recovery approaches

A meta recovery framework: positioning the ‘New Recovery’ movement and other recovery approaches

tional environments are characterized by life in small doses. Therapeutic community clients pro- gress through their journey to recovery in small steps, and they only assume bigger roles of respon- sibility as time progresses. In other words, reality confrontation is a stepped process with new clients having much less responsibility, with clients longer in treatment assuming more roles of responsibility. In trying to think about phases of recovery, and the suitability of models of recovery for particular client needs, we might consider Tough Recovery as an initial stage of recovery which pre-dates the cli- ent’s readiness to become a student of New Recov- ery. That is to say, we need to think about the transition from acute stages of illness to recovery interventions when the client has less severe suffer- ing. Ideally, all people on the pathway to recovery should have the opportunity for learning and edu- cation, much as Peplau envisages the hospital and health-care system as an educative endeavour. The reality however, is that many clients need to go through stages of recovery where their acute needs dictate a more active role on the part of profession- als before they are ready for more tender phases of recovery.
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Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

Fok I [38], they are a special family of restriction endonucleases that can recognize a specific sequence known as a restriction site along a dsDNA and they only cut one strand to leave a nick in dsDNA, but they all have strict requirements of the sequence and length in DNA probe design. To overcome the limitations of above nucleases, we alternatively utilize T7 exo to construct a new CESA system for facile, homogeneous and sensitive detection of human alkyladenine DNA glycosylase (hAAG) based on the controllable autocatalytic cleavage-mediated fluorescence recovery. Upon the specific cleavage of hairpin substrate (i.e., hairpin probe 1 (HP1)) at the damaged 2′-deoxyinosine site by hAAG and APE1, the hairpin structure of HP1 is unfolded to generate a DNA duplex. Trigger 1 built in the resultant DNA duplex may partially hybridize with HP2 through the toehold-mediated strand displacement reaction (TMSDR) to induce the T7 exo-catalyzed recycling cleavage of HP2 to release trigger 2. Trigger 2 is partially complementary with the signal probe (a 10-nt DNA fragment modified by a fluorophore (FAM) and a quencher (BHQ1) at its 5′ and 3′ ends), and it can induce the subsequent recycling cleavage of signal probes. Through two-recycling autocatalytic cleavage processes, large amounts of fluorophore molecules (i.e., FAM) are liberated from the FAM-BHQ1 fluorescence resonance energy transfer (FRET) pair, leading to the amplified fluorescence recovery. Taking advantage of the ubiquitous DNA repair mechanisms in vivo, the excellent features of T7 exo and the intrinsic superiorities of fluorescence strategy, the proposed method can provide a facile and robust biosensing platform for homogeneous detection of hAAG activity with high sensitivity and good specificity.
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Recovery of biologically active spleen focus-forming virus from molecularly cloned spleen focus-forming virus-pBR322 circular DNA by cotransfection with infectious type C retroviral DNA.

Recovery of biologically active spleen focus-forming virus from molecularly cloned spleen focus-forming virus-pBR322 circular DNA by cotransfection with infectious type C retroviral DNA.

Goat anti-Rauscher MuLV gp70 serum was used to precipitate cells cotransfected with undigested pBR322-SFFV recombinant DNA plus infectious FMuLV clone 57 DNA lane 1, cloned SFFV DNA rele[r]

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Epigenetic regulation of stroke recovery : changes in DNA methylation and micro-RNA regulation following stroke and EGF/EPO neurogenesis therapy

Epigenetic regulation of stroke recovery : changes in DNA methylation and micro-RNA regulation following stroke and EGF/EPO neurogenesis therapy

Following a stroke to the motor cortex, the brain undergoes a series of plastic responses in an attempt to recover from the resultant damage. These plastic responses include axonal sprouting and synaptic plasticity (Carmichael, 2006), as well as a limited degree of neurogenesis (Jin, et al., 2001) and migration of neural progenitors to the peri-infarct region (Kokaia, Thored, Arvidsson, & Lindvall, 2006). This enhanced plasticity allows the brain to re-arrange the sensorimotor maps of the damaged area and compensate, to a degree, for the function lost during the stroke (Carmichael, 2006). It has long been known that neural plasticity is a direct result of changes in the protein complement of a neuron (Sutton & Schuman, 2006), and that this change is driven by altered gene expression in response to synaptic activity (Cavallaro, Schreurs, Zhao, D'Agata, & Alkon, 2001). Recent evidence suggests that these altered levels of gene expression are under the control of at least two epigenetic mechanisms; DNA methylation and histone acetylation (Miller, Campbell, & Sweatt, 2008).
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Recovery capital pathways : modelling the components of recovery wellbeing

Recovery capital pathways : modelling the components of recovery wellbeing

In this study, we also tested the moderating effect of gender. Our results show that both recovery capital and wellbeing have the same meaning across groups. This is reflected in the constrained factor loadings (measurement weights) equal across groups (invariance). However, our results also found partial invariance of subscale intercepts. As noted above, women in our study tended to give higher scores in responses to (a) the 'citizenship' and 'housing and safety' sub-dimensions of social recovery capital, as well as in (b) the quality of life, support network and quality of accommodation sub-dimensions of wellbeing. Gendered differences have been observed in prior studies. For example, Kelly and Hoeppner (2013) argue that behaviour change for women is less associated with changes in social networks and more to do with the growth in abstinence self-efficacy. Likewise, women usually score lower in quality of life (Lev-Ran et al., 2012; Puigdollers et al., 2004). Thus it could also be the case that specific norms apply to this group, thus "biasing" the outcomes in their recovery journey.
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Citizenship and recovery: two intertwined concepts for civic recovery

Citizenship and recovery: two intertwined concepts for civic recovery

Background: Validation of the psychometric properties of a new measure of citizenship was required for a research project in the province of Quebec, Canada. This study was meant to study the interplay between recovery- and citizenship-oriented supportive employment. As recovery and citizenship were expected to be two related concepts, convergent validity between the Citizenship Measure (CM) and the Recovery Assessment Scale (RAS) was tested. Methods: Study objectives were to: 1) conduct exploratory factor analyses on the CM and confirmatory factor analysis on the RAS tools (construct validity), 2) calculate Cronbach ’ s alphas for each dimension emerging from objective 1 (reliability), and 3) calculate correlations between all dimensions from both tools (convergent validity). Data were collected from 174 individuals with serious mental illness, working in social firms. Serious mental illnesses include major depression, schizophrenia, bipolar disorder, obsessive compulsive disorder, panic disorder, post traumatic stress disorder and borderline personality disorder.
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Recovery of Exemplary Damages in the Absence of a Recovery of Compensatroy Damages

Recovery of Exemplary Damages in the Absence of a Recovery of Compensatroy Damages

Recovery of Exemplary Damages in the Absence of a Recovery of Compensatroy Damages SMU Law Review Volume 5 | Issue 4 Article 7 1951 Recovery of Exemplary Damages in the Absence of a Recovery of Compen[.]

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Recovery Home. MESA RECOVERY HOMES Chris cell

Recovery Home. MESA RECOVERY HOMES Chris cell

Community Bridges assumes no responsibility or liability for any community service providers on the list provided.. RECOVERY HOMES ADDRESS PHONE # GENDER /.[r]

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Dynamic Node Recovery in MANET for High Recovery Probability

Dynamic Node Recovery in MANET for High Recovery Probability

detection of identity frauds and prevents them. It chooses recovery path of trusted nodes only. In case of dual-link failures, BLME generates two mutual exclusive backup paths for recovery. R. Tuli et al. [5] presented an asynchronous checkpointing and optimistic message logging scheme. In order to overcome low storage capacity of a mobile host (MH), memory region of CH is utilized as stable storage of data by a MH. MH is then concerned with minimum information only, effectively utilizing its short storage. CH keeps a track record of messages for every node within its cluster. MH can voluntarily leave a cluster in order to conserve energy. This is termed as ‘disconnection’. The above approach is optimistic such that the MH does not wait for a process to be complete before sending the next message and assume an absolute logging process. The proposed scheme delivers better performance but at times, may create orphan messages. In the proposed OTMF (Objective Trust Management Framework), trustworthiness metric is a composite value of trust as well as confidence value of a node [24]. It is an objective computation, where confidence value refers to the accuracy of trust value. Comparison with the existing reputation-based framework has been made depicting the necessity to include confidence value in the computation of trustworthiness because its presence and absence changes the trust value invariably. Although both the approaches provide admirable impartial conduct of node towards its neighbors, but more rational framework can be built using the proposed model.
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