Optical Thickness-Encoded Suspension Array for High-Throughput Multiplexed Gene Detection

We proposed a coding and decoding method of suspension array (SA) based on micro-quartz pieces (MQPs) with different optical thicknesses. The capture probes (cDNA) were grafted onto the surfaces of MQPs and specifically recognized and combined with the partial sequence of the target DNA (tDNA) to form a MQP-cDNA-tDNA complex. Quantum dot-labeled signal probes were then used to specifically recognize and bind another portion of the tDNA in the complex to form a double-probe sandwich structure. This optical thickness-encoded SA can be decoded and detected by a dual-wavelength digital holographic phase fluorescence microscope system. We conducted a series of DNA molecule detection experiments by using this encoding method. Control experiments confirmed the specificity of optical thickness-encoded SA in DNA detection. The concentration gradient experiments then demonstrated the response of the MQPs based SA to analyte concentration. Finally, we used the encoding method to detect three types of DNA in a single sample and confirmed the feasibility of the proposed optical thickness-encoded SA in multiplexed DNA detection. The detection results are stable, and the detection exhibits high specificity and good repeatability.

Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators

Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for arthropod biodiversity assessments from soil. Processing 15 individually collected soil samples recovered significantly higher median richness (488-614 sequence variants) than pooling the same number of samples (165-191 sequence variants) prior to DNA extraction, and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Beta diversity was robust to changes in methodological regimes. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

Quality assessment of cryopreserved biospecimens reveals presence of intact biomolecules

Recapitulation of tumor features in isolated biomolecules is preeminently dependent on obtaining reliable quality biospecimen. Moreover, quality assessment of biobanked specimens at regular intervals is an essential intervention for carrying out effective translational and clinical research. In the current study, genomic DNA was extracted from 140 fresh frozen tissues of oral, breast and colorectal specimens cryopreserved over a period of 3 to 8 months (short term) and 3 to 4 years (long term). Quantification of genomic DNA by absorption and fluorescence spectroscopy confirmed high concentration while qualitative analysis by gel electrophoresis showed intact bands for 94% and 87% of short- and long-term cohorts, respectively. PC-LDA based classification of Raman spectra showed overlapping groups of both cohorts suggesting the quality of DNA being preserved irrespective of storage period. To the best of our knowledge this is the first Indian biobank study reporting quality analysis of biospecimens cryopreserved at different time periods.

Clean and clear (out): A neat method for the recovery of latent fingermarks from crime-scenes

Crime-scenes are the heart of any investigation in terms of recovery of key forensic evidence - fingermarks and DNA. Yet, quite often, the operational work of the forensic units, in which different chemicals and reagents for fingermarks development are applied, can also be highly destructive to the property and the environment. Hence, for both ecological and intelligence purposes, an operational method that minimizes that damage would be ideal. In this study, an "out-of-the-box" approach is proposed; rather than working at the crime scene itself, gel-lifters were used as a transferring tool for the latent forensic evidence, fingermarks and DNA, to be developed by applying black wet-powder (Wetwop®) in a controlled laboratory environment, leaving the crime-scene undisturbed. The results show a promising potential, as this indirect method proved to be robust and successful for non-porous surfaces, and even for aged fingermarks. In addition, this study gave a new perspective into the accepted notion regarding the difference between male and female donors, showing a direct correlation of the size and weight of the hands to the natural pressure applied by the donor. Moreover, the indirect nature of the method highlights the importance of the interaction between the type of surface and the latent fingermark constituents, primarily water, and its effect on the survivability and quality of the developed fingermark. Due to the growing demand of keeping crime scenes and exhibits unharmed by both police and intelligence forces, the new approach of this application provides a valuable asset for future operational field-work.

Tears and Eyewear in Forensic Investigation-A Review

Body fluid analysis has played a crucial role in ascertaining various characteristics and has greatly aided in reconstructing events during crime scene investigation. It is often presumed that crimes that involve violence and mental disturbances such as murder or sexual assault provide good sources of body fluids such as blood, saliva, semen, vaginal secretions, urine and tears. Tears are secreted in response to any emotional or stressful situations and may be found deposited on surfaces such as bedding, tissue paper or cloth. In the absence of the commonly noted body fluids such as blood or saliva, tears can play an important role that can lead to personal identification by examining the biochemistry and molecular aspects to obtain a full DNA profile. Additionally, identification of an individual may be done by carefully observing certain unique eye characteristics such as heterochromia which is highly individualistic. Characteristics of eyewear such as spectacles and contact lenses have unique properties and prescription criteria for correcting an individual's eyesight that can provide vital clues in understanding the visual ability of an individual. In crime scene investigation, the presence or absence of eyewear provides immense evidentiary value that has greatly aided in solving cases such as Janet Abaroa's Murder. This paper provides a systematic review of the possibility of using tears and eyewear for the purpose of forensic investigation and to statistically support the inferences with prescription databases which may be initiated across different populations. Forensic Optometry is yet to get streamlined along with the routinely followed investigative techniques and scientifically explored although no standard protocols exist to analyse eyewear. The use of behavioural optometry is gaining attention in the context of driving laws of different countries and is a simple but powerful indicator of abnormal behaviour. It is speculated that the last seen image referred to as an 'Optogram' of an individual may be captured in the retina since our eyes functions like a camera. Although this claim is considerably unexplored, it is quite possible that the last seen image of a criminal, objects or a place may be noted that can positively help in linking individuals at the scene of crime or identify the primary crime location. In this review, the potential for new insights into the analysis of tears, eye and eyewear characteristics have been explored.

Characterisation of Anopheles strains used for laboratory screening of new vector control products

BACKGROUND

Insecticides formulated into products that target Anopheles mosquitos have had an immense impact on reducing malaria cases in Africa. However, resistance to currently used insecticides is spreading rapidly and there is an urgent need for alternative public health insecticides. Potential new insecticides must be screened against a range of characterized mosquito strains to identify potential resistance liabilities. The Liverpool School of Tropical Medicine maintains three susceptible and four resistant Anopheles strains that are widely used for screening for new insecticides. The properties of these strains are described in this paper.

METHODS

WHO tube susceptibility bioassays were used for colony selection and to screen for resistance to the major classes of public health insecticides. Topical and tarsal contact bioassays were used to produce dose response curves to assess resistance intensity. Bioassays with the synergist piperonyl butoxide were also performed. Taqman™ assays were used to screen for known target site resistance alleles (kdr and ace-1). RT-qPCR was used to quantify expression of genes associated with pyrethroid resistance.

RESULTS

Pyrethroid selection pressure has maintained resistance to this class in all four resistant strains. Some carbamate and organophosphate resistance has been lost through lack of exposure to these insecticide classes. The Anopheles gambiae (sensu lato) strains, VK7 2014, Banfora M and Tiassalé 13 have higher levels of pyrethroid resistance than the An. funestus FUMOZ-R strain. Elevated expression of P450s is found in all four strains and the 1014F kdr mutation is present in all three An. gambiae strains at varying frequencies. Tarsal contact data and overexpression of CYP4G16 and SAP2 suggest penetration barriers and/or sequestration also confer resistance in Banfora M.

CONCLUSIONS

Continual selection with deltamethrin has maintained a stable pyrethroid-resistant phenotype over many generations. In conjunction with a standardized rearing regime, this ensures quality control of strains over time allowing for robust product comparison and selection of optimal products for further development. The identification of multiple mechanisms underpinning insecticide resistance highlights the importance of screening new compounds against a range of mosquito strains.

Validation of a Targeted PCR Method for Raw and Processed Botanical Material Identification: An Example Using Matricaria chamomilla (Chamomile)

Background: A requirement of current good manufacturing practices for dietary supplements is that manufacturers must identify their dietary ingredients. DNA-based methods can provide species-level authentication that may sometimes be difficult to achieve using conventional morphological and chemical analysis methods. However, because of varying levels of DNA degradation in botanical materials, many commercial tests fail to generate consistent test results across all types of botanical materials. AOAC published guidelines for validation of botanical identification methods and proposed probability of identification (POI) as a method performance parameter. However, few DNA-based botanical authentication methods in the literature follow these guidelines and evaluate POI. Objective: To provide a targeted PCR method validation example that follows AOAC guidelines for validation of botanical identification methods. Methods: Using Matricaria chamomilla (chamomile) as an example, we performed a single-laboratory validation for a targeted PCR method that aimed to identify both raw and processed chamomile materials. The performance parameters of the test were evaluated by carrying out an inclusivity/exclusivity study and a Specified Superior Test Material/Specified Inferior Test Material study to demonstrate that the method’s POI meets industry requirements. Results: The chamomile samples were identified by the method and achieved a POI greater than 0.9 with respect to all types of chamomile botanical materials. Conclusions: The method was validated for DNA-based identification of raw and processed chamomile materials, such as sterilized powders and extracts. Highlights: This work will provide insight for laboratories and manufacturers that aim to develop and validate DNA-based botanical identification methods.

Small-Scale Isolation of Bacterial Artificial Chromosome (BAC) DNA and Verification by Polymerase Chain Reaction (PCR)

In this protocol, small amounts of selected bacterial artificial chromosome (BAC) DNAs are prepared from 5-mL cultures of the Escherichia coli host transformed with the BAC clone. DNA is isolated by an adaptation of the alkaline lysis method. The yield is 0.1-0.4 µg, and the BAC DNA is suitable for analysis by polymerase chain reaction (PCR). Considerations for clone selection are also addressed.

Purification of silica-free DNA and characterization of its role in coagulation

BACKGROUND

Although extracellular DNA has been reported to activate coagulation, its direct effects and consequent interpretations have recently been questioned because of silica and polyphosphate (polyP) contaminations when DNA is isolated using common silica-based kits.

OBJECTIVES

To identify and characterize alternative methods of isolating DNA that is free of silica with functionally undetectable levels of polyP.

METHODS

DNA was isolated from the whole blood or buffy coat using three different DNA isolation kits: (a) the silica-based QIAGEN QIAMP DNA Blood mini kit (silica-DNA), (b) the non-silica-based QIAGEN PAXgene Blood DNA kit (PAX-DNA), and (c) the non-silica-based QuickGene DNA whole blood kit large (DBL-DNA). The procoagulant properties of DNA were assessed by thrombin generation and plasma clotting assays. A polyP detection assay was used to detect polyP contamination.

RESULTS AND CONCLUSIONS

Unlike the isolated DNA, commercially available calf thymus DNA contains thrombinlike amidolytic activity. The PAX-DNA and DBL-DNA did not contain silica nor functionally detectable polyP as contaminants. Both PAX- and DBL-DNA were procoagulant in a dose-dependent manner, which is neutralized with deoxyribonuclease I (DNase I). Thus, we recommend the use of PAX-DNA or DBL-DNA for functional studies to investigate the role of extracellular DNA.

Increasing DNA Isolation Performance from Blood Cells Using a Modified Commercial Low-Cost Reagent

BACKGROUND

Genomic studies facilitate comprehension of the pathophysiology, diagnosis, and treatment of chronic diseases. Such studies require sufficient and good quality DNA isolated from a large number of blood samples. This study attempts to obtain a high-quality genomic DNA isolated from a large number of blood samples using a simple and cheap method.

METHODS

The EasyPure® Genomic DNA Kit (Transgen Biotech) was modified to increase the amount of DNA recovery: a few steps and two additional column elutions were added to the original manufacturer´s procedure.

RESULTS

The amount of DNA isolated from frozen blood samples increased by an average of 56%. Its 260/280 ratio and electrophoretic mobility properties make it suitable for genomic studies.

CONCLUSIONS

A relatively low-cost commercial column and a simple modification of the manufacturer´s protocol, provided a simple and cheap procedure to isolate high-quality DNA from a large number of blood samples suitable for genomic studies.

Comparison of four DNA extraction and three preservation protocols for the molecular detection and quantification of soil-transmitted helminths in stool

Background

A DNA extraction and preservation protocol that yields sufficient and qualitative DNA is pivotal for the success of any nucleic acid amplification test (NAAT), but it still poses a challenge for soil-transmitted helminths (STHs), including Ascaris lumbricoides, Trichuris trichiura and the two hookworms (Necator americanus and Ancylostoma duodenale). In the present study, we assessed the impact of different DNA extraction and preservativation protocols on STH-specific DNA amplification from stool.

Methodology and principal findings

In a first experiment, DNA was extracted from 37 stool samples with variable egg counts for T. trichiura and N. americanus applying two commercial kits, both with and without a prior bead beating step. The DNA concentration of T. trichiura and N. americanus was estimated by means of qPCR. The results showed clear differences in DNA concentration across both DNA extraction kits, which varied across both STHs. They also indicated that adding a bead beating step substantially improved DNA recovery, particularly when the FECs were high. In a second experiment, 20 stool samples with variable egg counts for A. lumbricoides, T. trichiura and N. americanus were preserved in either 96% ethanol, 5% potassium dichromate or RNAlater and were stored at 4°C for 65, 245 and 425 days. DNA was extracted using the DNeasy Blood & Tissue kit with a bead beating step. Stool samples preserved in ethanol proved to yield higher DNA concentrations as FEC increased, although stool samples appeared to be stable over time in all preservatives.

Conclusions

The choice of DNA extraction kit significantly affects the outcome of NAATs. Given the clear benefit of bead beating and our validation of ethanol for (long-term) preservation, we recommend that these aspects of the protocol should be adopted by any stool sampling and DNA extraction protocol for downstream NAAT-based detection and quantification of STHs.

DNA-based tools are increasingly being used for the diagnosis of intestinal worm infections in both clinical and research laboratories. However, recovering DNA from intestinal worm eggs in stool remains a challenge since this DNA is protected by a very rigid egg shell. Furthermore, stool contains inhibitors that can affect test results and these should be removed during DNA extraction. Prior to DNA extraction, samples are often preserved, but the impact of the type of preservatives and the duration of preservation remains poorly studied. In the present study, we assessed the impact of four DNA extraction and three preservation protocols on the downstream performance of a DNA-based diagnostic tool for intestinal worms. We found significant differences in DNA recovery across the DNA and preservation protocols, but DNA from worm eggs in stool proved to be stable over time in all preservatives.

Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

BACKGROUND

Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library.

METHODS

We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels.

RESULTS

A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6-6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels.

CONCLUSIONS

Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.

Cleaning a crime scene 2.0-what to do with the bloody knife after the crime?

The persistence of DNA on washed items as well as the DNA transfer has become a major subject of research in recent years, especially after the detectability of minor DNA traces was heavily increased by sensitive analysis methods. Nowadays, the attribution of a DNA trace to an individual is only rarely questioned, whereas the way of application of this DNA to an item is subject to much discussion and speculation. Additionally, the removal of DNA by cleaning or its possible persistence on an item despite a cleaning process are often important problems in court. The aim of this study was to investigate whether DNA traces (blood, saliva, epithelial cells) on different objects (knives, plates, glasses, and plastic lids) can persist on the surface despite cleaning by different methods like hand-washing or the use of a dishwasher. In total, 120 samples were collected from artificially constructed blood, saliva, and epithelial cell stains on objects with smooth surfaces after washing and analyzed by STR amplification. Samples taken after rinsing or hand-washing resulted mainly in complete DNA profiles (62.5% of samples), while cleaning in the dishwasher rendered almost everything completely DNA-free. Since in the hand-washing experiments a secondary transfer of DNA through the water could not be ruled out, additional transfer experiments were conducted with blood and saliva samples on plates. Here, a carryover of DNA traces could be demonstrated up to the fifth washed item.

Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant

This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L^-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.

Cytoplasmic DNA can be detected by RNA fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) can be used for the intracellular detection of DNA or RNA molecules. The detection of DNA sequences by DNA FISH requires the denaturation of the DNA double helix to allow the hybridization of the fluorescent probe with DNA in a single stranded form. These hybridization conditions require high temperature and low pH that can damage RNA, and therefore RNA is not typically detectable by DNA FISH. In contrast, RNA FISH does not require a denaturation step since RNA is single stranded, and therefore DNA molecules are not detectable by RNA FISH. Hence, DNA FISH and RNA FISH are mutually exclusive. In this study, we show that plasmid DNA transiently transfected into cells is readily detectable in the cytoplasm by RNA FISH without need for denaturation, shortly after transfection and for several hours. The plasmids, however, are usually not detectable in the nucleus except when the plasmids are efficiently directed into the nucleus, which may imply a more open packaging state for DNA after transfection. This detection of plasmid DNA in the cytoplasm has implications for RNA FISH experiments and opens a window to study conditions when DNA is present in the cytoplasm.

Highly ordered 3D electrochemical DNA biosensor based on dual orientation controlled rolling motor and graftable tetrahedron DNA

Herein, a robust and highly ordered three-dimensional electrochemical DNA (3D E-DNA) biosensor was proposed, and its orientation was controlled from top down by poly adenine oligonucleotides (polyA-ODNs)-mediated rolling motor (PRM) and graftable tetrahedron DNA (GTD). The GTD with a grafting domain was immobilized on the electrode surface to construct a well-organized sensing interface and controlled the orientation and distribution of the whole system at the "bottom" of this biosensor. The polyA-ODNs regulated the direction and density of the leg DNA attached on PRM at the "top" of the biosensor. The motion was achieved through the target induced cyclic cleaving, which triggered the motor rolling rather than walk. Impressively, the duplex strand DNA (dsDNA) formed after grafting, as a girder, provided a stable support to the soft long single strand (ssDNA), which facilitated the formation of the catalytic center, elevated the efficiency of the rolling cleavage. Under the optimal conditions, the designed biosensor exhibited a lower limit of 0.17 nM and wide linear range from 0.5 nM to 1.5 μM for adenosine rapid detection. Unique dual orientation regulated characteristics of the system increased the probability hybridization enormously and improved the motion efficiency significantly, which offered new avenue of DNA nanomachines development in biosensor platform.

Removing DNA Contamination from RNA Samples by Treatment with RNase-Free DNase I

RNA samples prepared using monophasic lysis reagents may contain small amounts of contaminating genomic DNA, which must be removed if the RNA will be used in subsequent analyses such as reverse transcriptase-polymerase chain reaction (RT-PCR) or quantitative real-time RT-PCR. In addition, the presence of contaminating DNA can render the quantitative determination of RNA in a sample inaccurate. The most common and effective method for removing trace to moderate amounts of DNA contamination from RNA samples is digestion with DNase I, as described here.

A three-gene DNA methylation biomarker accurately classifies early stage prostate cancer

BACKGROUND

We identify and validate accurate diagnostic biomarkers for prostate cancer through a systematic evaluation of DNA methylation alterations.

MATERIALS AND METHODS

We assembled three early prostate cancer cohorts (total patients = 699) from which we collected and processed over 1300 prostatectomy tissue samples for DNA extraction. Using real-time methylation-specific PCR, we measured normalized methylation levels at 15 frequently methylated loci. After partitioning sample sets into independent training and validation cohorts, classifiers were developed using logistic regression, analyzed, and validated.

RESULTS

In the training dataset, DNA methylation levels at 7 of 15 genomic loci (glutathione S-transferase Pi 1 [GSTP1], CCDC181, hyaluronan, and proteoglycan link protein 3 [HAPLN3], GSTM2, growth arrest-specific 6 [GAS6], RASSF1, and APC) showed large differences between cancer and benign samples. The best binary classifier was the GAS6/GSTP1/HAPLN3 logistic regression model, with an area under these curves of 0.97, which showed a sensitivity of 94%, and a specificity of 93% after external validation.

CONCLUSION

We created and validated a multigene model for the classification of benign and malignant prostate tissue. With false positive and negative rates below 7%, this three-gene biomarker represents a promising basis for more accurate prostate cancer diagnosis.

Recovery of DNA from Agarose Gels Using Glass Beads

This DNA recovery protocol uses glass beads and a solution of sodium iodide/sodium sulfite as a chaotropic agent to disrupt the agarose gel.

Assessment of the Yfiler® Plus PCR amplification kit for the detection of male DNA in semen-negative sexual assault cases

The ability to detect male epithelial cells deposited during digital penetration or penile penetration without ejaculation is limited by the sensitivity of the Y-STR profiling kit. In this study, the relative profiling success of the Thermofisher Yfiler® Plus kit was compared to its predecessor, AmpFlSTR Yfiler®, for 104 semen-negative sexual assault samples from casework at Forensic Science SA, Adelaide, South Australia. Yfiler Plus generated allele information in 25% more samples than Yfiler and gave a higher recovery of informative alleles in all but two samples where detectable male DNA was present. Where a profile was obtained in both kits, 92% of samples gave a higher percentage of informative loci with Yfiler Plus compared to Yfiler. Yfiler Plus also resolved DNA mixtures in 15 samples as compared to 1 sample with Yfiler. Detection of male DNA with the Quantifiler™ Trio DNA Quantification kit was shown to correlate with a successful profiling outcome with Yfiler Plus. The success of profiling with Yfiler Plus was independent of the time elapsed between the alleged offence and the sample being collected, the type of sexual penetration which occurred, and the anatomical origin of the sample.

Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection

Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 10⁴ cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.

Multilevel regression modeling for aneuploidy classification and physical separation of maternal cell contamination facilitates the QF-PCR based analysis of common fetal aneuploidies

Background

The quantitative fluorescent polymerase chain reaction (QF-PCR) has proven to be a reliable method for detection of common fetal chromosomal aneuploidies. However, there are some technical shortcomings, such as uncertainty of aneuploidy determination when the short tandem repeats (STR) height ratio is unusual due to a large size difference between alleles or failure due to the presence of maternal cell contamination (MCC). The aim of our study is to facilitate the implementation of the QF-PCR as a rapid diagnostic test for common fetal aneuploidies.

Methods

Here, we describe an in-house one-tube multiplex QF-PCR method including 20 PCR markers (15 STR markers and 5 fixed size) for rapid prenatal diagnosis of chromosome 13, 18, 21, X and Y aneuploidies. In order to improve the aneuploidy classification of a given diallelic STR marker, we have employed a multilevel logistic regression analysis using "height-ratio" and "allele-size-difference" as fixed effects and "marker" as a random effect. We employed two regression models, one for the 2:1 height ratio (n = 48 genotypes) and another for the 1:2 height ratio (n = 41 genotypes) of the trisomic diallelic markers while using the same 9015 genotypes with normal 1:1 height ratio in both models. Furthermore, we have described a simple procedure for the treatment of the MCC, prior DNA isolation and QF-PCR analysis.

Results

For both models, we have achieved 100% specificity for the marker aneuploidy classification as compared to 98.60% (2:1 ratio) and 98.04% (1:2 ratio) specificity when using only the height ratio for classification. Treatment of the MCC enables a successful diagnosis rate of 76% among truly contaminated amniotic fluids.

Conclusions

Adjustment for the allele size difference and marker type improves the STR aneuploidy classification, which, complemented with appropriate treatment of contaminated amniotic fluids, eliminates sample re-testing and reinforces the robustness of the QF-PCR method for prenatal testing.

Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing

Human dental remains encountered in criminal casework evidence, missing person cases, or mass disaster tragedies provide a valuable sample source for DNA typing when suitable soft tissue is unavailable. Using traditional methods, teeth samples can be challenging to process, resulting in low-quantity and/or quality nuclear DNA and insufficient profiles for comparisons. This study examines the performance of a three-part nuclear DNA analysis workflow for teeth samples based on (1) improved dental tissue recovery using the Dental Forensic Kit (DFK^MR) (Universidad de los Andes) and DNA extraction with QuickExtract™ FFPE DNA Extraction Kit (Lucigen®), (2) quantification with InnoQuant® HY (InnoGenomics Technologies) for sensitive assessment of total human and male DNA quantity/quality, and (3) massively parallel sequencing for simultaneous genotyping of 231 short tandem repeat (STR) and single-nucleotide polymorphism (SNP) markers with the ForenSeq® DNA Signature Prep Kit (Verogen, Inc.). Initial evaluation of artificially degraded blood samples (n = 10) achieved highly sensitive and informative quantification results with InnoQuant® HY, enabling successful first pass genotyping with the MiSeq FGx® System. Twenty-three STR alleles (out of 85) and 70 identity informative SNP loci (out of 94) were recovered from two pg total long target DNA input (0.86 ng total short target input) and an InnoQuant degradation index (DI) of 460 (severely degraded). The three-part workflow was subsequently applied to teeth samples (dental pulp, root cement tissues; n = 13) with postmortem intervals (PMI) of the teeth ranging from 8 days to approximately 6 months. Informative SNP and STR DNA profiles were obtained, to include 78 STR alleles and 85 identity informative SNP loci typed (of 94 total SNP targets) in a 1 month, four-day PMI root cement sample with one pg total long target DNA input and a DI of 76. These data indicate successful performance of the proposed workflow from degraded DNA from teeth samples.

First Report of the Introduction of an Exotic Tick, Amblyomma coelebs (Acari: Ixodidae), Feeding on a Human Traveler Returning to the United States from Central America

Introduction of ticks into the United States that can carry disease-causing pathogens to humans, companion animals, and wildlife has accelerated in recent years, mostly due to globalization, frequency of travel, and a rise in legal and illegal animal trades. We hereby report for the first time introduction of a live fully engorged Amblyomma coelebs feeding on a human into the United States from Central America. Amblyomma coelebs is geographically distributed in the Neotropical region and reaches the southern states of Mexico. This species is capable of transmitting a number of pathogens of public health and veterinary importance including spotted fever group rickettsiae, raising concern that A. coelebs, if it became established in the United States, might also be able to carry these pathogens. Considering the risks of exotic ticks as vectors of numerous pathogens and their potential to establish new populations under conducive climatic and habitat conditions, rigorous inspection practices of imported livestock and pet animals at ports of entry are vital. It is also important for travelers and practitioners to develop a heightened awareness of the public health risks associated with the unintended importation of exotic ticks and the potential such parasites have for breaching United States biosecurity defenses.

Genetics and telemetry indicate unexpected movements among structured populations for Brachyplatystoma platynemum in the Amazon

The genetic analysis of Brachyplatystoma platynemum individuals sampled from the lower Madeira River reinforces the existence of two structured populations in the Amazon Basin (Madeira and Amazon populations). However, the recapture of an individual from the Amazon population in the Solimões River, which was telemetry-tagged in the Madeira River after the damming, indicates that fish from the Amazon population move between the two river systems. This has not yet been observed, however, in the Madeira River population, which is currently divided and isolated in the lower and upper Madeira River by the construction of two dams.