Prenatal Detection of Chromosome Aneuploidy by Quantitative Fluorescence PCR

Autosomal chromosome aneuploid pregnancies that survive to term, namely, trisomies 13, 18, and 21, account for 89% of chromosome abnormalities with a severe phenotype identified in prenatal samples. They are traditionally detected by full karyotype analysis of cultured cells. The average reporting time for a prenatal karyotype analysis is approximately 14 days, and in recent years, there has been increasing demand for more rapid prenatal results with respect to the common chromosome aneuploidies, to relieve maternal anxiety and facilitate options in pregnancy. The rapid tests that have been developed negate the requirement for cultured cells, instead directly testing cells from the amniotic fluid or chorionic villus sample, with the aim of generating results within 48 h of sample receipt. Interphase fluorescence in situ hybridization is the method of choice in some genetic laboratories, usually because the expertise and equipment are readily available. However, a quantitative fluorescence (QF)-PCR-based approach is now widely used and reported as a clinical diagnostic service in many studies. It may be used as a stand-alone test or as an adjunct test to full karyotype or array CGH analysis, which scan for other chromosome abnormalities not detected by the QF-PCR assay.

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition

Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.

Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits

Oral health and disease are known to be influenced by complex interactions between environmental (e.g., social and behavioral) factors and innate susceptibility. Although the exact contribution of genomics and other layers of "omics" to oral health is an area of active research, it is well established that the susceptibility to dental caries, periodontal disease, and other oral and craniofacial traits is substantially influenced by the human genome. A comprehensive understanding of these genomic factors is necessary for the realization of precision medicine in the oral health domain. To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation of millions of genetic polymorphisms for association with oral and craniofacial traits. Specifically, genome-wide association studies (GWAS) of dental caries and periodontal disease have provided initial insights into novel loci and biological processes plausibly implicated in these two common, complex, biofilm-mediated diseases. This paper presents a summary of protocols, methods, tools, and pipelines for the conduct of GWAS of dental caries, periodontal disease, and related traits. The protocol begins with the consideration of different traits for both diseases and outlines procedures for genotyping, quality control, adjustment for population stratification, heritability and association analyses, annotation, reporting, and interpretation. Methods and tools available for GWAS are being constantly updated and improved; with this in mind, the presented approaches have been successfully applied in numerous GWAS and meta-analyses among tens of thousands of individuals, including dental traits such as dental caries and periodontal disease. As such, they can serve as a guide or template for future genomic investigations of these and other traits.

Nucleic Acid Extraction from Human Biological Samples

Nucleic acid isolation is often the starting point for all downstream experiments in biomedical research. It is therefore the most crucial step in any molecular technique. DNA and RNA extraction follow protocols with standardized reagents, many of which are available in quality-controlled commercial kits. Irrespective of the protocol, successful extraction of high-quality nucleic acid from biological tissues requires sufficient disruption of the tissue and cellular structures, denaturation of nucleoprotein complexes, inactivation of nucleases, and nucleic acid purification. These steps can be modified based on nucleic acid of interest and biological sample source. This chapter addresses DNA and RNA extraction from a variety of sample and tissue types, including saliva, and formalin-fixed, paraffin-embedded tissues, which are often archived in clinical pathology laboratories. Special considerations and common pitfalls of each protocol will also be discussed, as will nucleic acid quantitation techniques.

Measurement of Leukemic B-Cell Growth Kinetics in Patients with Chronic Lymphocytic Leukemia

Cell proliferation plays a central role in the pathogenesis of every neoplastic disease as well as many other types of illness. Labeling of newly replicated DNA with deuterium (²H), a nonradioactive isotope of hydrogen, administered to the patients in drinking water (²H₂O) is a safe and reliable method to measure the in vivo birth rates of cells. Here, we describe a protocol to measure chronic lymphocytic leukemia B-cell birth/proliferation and death rates over time using this approach.

PCR GeneScan and Heteroduplex Analysis of Rearranged Immunoglobulin or T-Cell Receptor Genes for Clonality Diagnostics in Suspect Lymphoproliferations

Assessment of the presence of clonal lymphoproliferations via polymerase chain reaction (PCR)-based analysis of rearranged immunoglobulin (IG) or T-cell receptor (TR) genes is a valuable method in the diagnosis of suspect lymphoproliferative disorders. Additionally, this methodology can be used for evaluating dissemination of lymphoma cells and for studying the clonal relationship between multiple (different locations) or consecutive (over time) lymphomas. Here we describe an integrated approach to assess clonality via analysis of Ig heavy chain (IGH), Ig kappa (IGK), TCR beta (TRB), and TCR gamma (TRG) gene rearrangements, based on the standardized multiplex PCRs as originally developed by the European BIOMED-2 consortium. The described protocol covers the pre-analytical phase of DNA isolation (from formalin-fixed paraffin-embedded and fresh tissues, body fluids, peripheral blood, and bone marrow), the analytical phase of PCR GeneScan and heteroduplex analysis, and the post-analytical interpretation of the obtained profiles, following established guidelines.

DNA Methylation Analysis

DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal biology and diseases including cancer. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC), and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the methylation regulation. Genome-wide analyses such as microarrays and next-generation sequencing technologies have been used to assess large fractions of the methylome. A number of different quantitative approaches have also been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing, pyrosequencing etc. These methods have been used to generate base-resolution maps of 5mC and its oxidation derivatives in genomic samples. The focus of this chapter is to provide the methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.

Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate

DNA isolated from ancient bones and teeth comprises a mixture of microbial contamination and DNA from the organism under study. In addition, analyses of ancient human remains are often complicated by contamination with present-day human DNA, which can be introduced during excavation and subsequent handling of the specimens. In most cases, the relative abundance of contaminant DNA is much greater than that of the target organism. Here we present two techniques for reducing the proportion of contaminant DNA in bones and teeth. The first and most efficient technique uses a sodium hypochlorite (bleach) pretreatment to destroy contaminant DNA that may be bound or otherwise attached to the surface of bone/tooth powder. The second, less destructive pretreatment uses a phosphate buffer to release surface-bound DNA.

A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation

Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.

Molecular Sexing of the White-Winged Guan (Penelope albipennis) and Other Wild Birds of the North of Peru

The use of accurate and reliable techniques for sex determination of wild birds is of special importance in captive breeding programs, especially in birds with monogamous, aggressive behavior, with absence of copulation, and with a low hatching rate. Using PCR, we evaluated the relative efficacy of primers HPF/HPR and CHD1Wr/NP/CHD1Zr in the amplification of the chromo-helicase-DNA binding 1 (CHD1) gene for sex determination in Penelope albipennis and 8 other species of cracids, 4 species of falconids, 4 species of accipitrids, and 3 species of psittacines. Primer effectiveness was compared using previously sexed bird samples. The HPF/HPR primer set was found to demonstrate a better performance and reliability. Therefore, these primers should be used to determine the sex of juvenile birds to avoid or minimize incompatibilities during the selection of potential breeding pairs.

First report of molecular characterization and sequence phylogenetic analysis of Linguatula serrata from India

Linguatula serrata is a pentastomid which is worldwide in distribution. However, a very few references are reported from India. In the present study, the cox I gene of L. serrata nymphs, originally isolated from mesenteric lymph nodes of buffaloes, was amplified and custom sequenced. Based on sequence analysis, two haplotypes were noticed and were subsequently submitted in NCBI database. The sequences were also compared with the other sequences available in the pubmed and phylogenetic analysis coupled with nucleotide homologies were commutated. The studied Indian isolates were found closer to Bangladesh and Iran isolates. This is the first report of molecular characterization of L. serrata from India.

A pilot study for establishing quality indicators in molecular diagnostics according to the IFCC WG-LEPS initiative: preliminary findings in China

Background

Quality indicators (QIs) are crucial tools in measuring the quality of laboratory services. Based on the general QIs of the Working Group “Laboratory Errors and Patient Safety (WG-LEPS)” of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), specific QIs have been established in order to monitor and improve the quality of molecular diagnostics, and to assess the detection level of associated disease.

Methods

A survey was conducted on 46 independent commercial laboratories in China, investigated using questionnaires and on-site inspections. Specific QIs established were mainly based on the specific laboratory work-flow for molecular diagnoses. The specific QI results from three volunteer laboratories were collected and used to validate their effectiveness.

Results

Of the 46 laboratories participating in the study, 44 (95.7%), conducted molecular diagnostics. Of 13 specific established QIs, six were priority level 1, and seven, priority level 3. At pre-evaluation of data from the three volunteering laboratories, it was found that the newly classified specific QIs had outstanding advantages in error identification and risk reduction.

Conclusions

Novel specific QIs, a promising tool for monitoring and improving upon the total testing process in molecular diagnostics, can effectively contribute to ensuring patient safety.

Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian reservoir

Biodiversity has to be accurately evaluated to assess more precisely possible dam effects on fish populations, in particular on the most biodiverse rivers such as the Mekong River. To improve tools for fish biodiversity assessment, a methodological survey was performed in the surroundings of a recent hydropower dam in the Mekong basin, the Nam Theun 2 project. Results of two different approaches, experimental surface gillnets capture and environmental DNA metabarcoding assays based on 12S ribosomal RNA and cytochrome b, were compared during 3 years (2014–2016). Pitfalls and benefits were identified for each method but the combined use of both approaches indisputably allows describing more accurately fish diversity around the reservoir. Importantly, striking convergent results were observed for biodiversity reports. 75% of the fish species caught by gillnets (62/82) were shown by the metabarcoding study performed on DNA extracted from water samples. eDNA approach also revealed to be sensitive by detecting 30 supplementary species known as present before the dam construction but never caught by gillnets during 3 years. Furthermore, potential of the marker-genes study might be underestimated since it was not possible to assign some sequences at lower taxonomic levels. Although 121 sequences were generated for this study, a third of species in the area, that exhibits high endemism, are still unknown in DNA databases. Efforts to complete local reference libraries must continue to improve the taxonomic assignment quality when using the non-invasive and promising eDNA approach. These results are of broader interest because of increasing number of hydropower projects in the Mekong Basin. They reveal the crucial importance to sample tissues/DNA of species before dam projects, i.e. before the species could become endangered and difficult to catch, to obtain more precise biomonitoring in the future as we believe eDNA metabarcoding will rapidly be integrated as a standard tool in such studies.

Exploring the influence from whole blood DNA extraction methods on Infinium 450K DNA methylation

Genome-wide DNA methylation studies are becoming increasingly important in unraveling the epigenetic basis of cell biology, aging and human conditions. The aim of the present study was to explore whether different methods for extracting DNA from whole blood can affect DNA methylation outcome, potentially confounding DNA methylation studies. DNA was isolated from healthy blood donors (n = 10) using three different extraction methods (i.e. two automatic extractions methods based on magnetic beads or isopropanol precipitation, and manual organic extraction). DNA methylation was analyzed using the Infinium HumanMethylation450 Bead Chip (Infinium 450K) (n = 30 samples in total), which is a frequently used method in genome-wide DNA methylation analyses. Overall, the different extraction methods did not have a significant impact on the global DNA methylation patterns. However, DNA methylation differences between organic extraction and each of the automated methods were in general larger than differences between the two automated extraction methods. No CpG sites or regions reached genome-wide significance when testing for differential methylation between extraction methods. Although this study is based on a small sample, these results suggest that extraction method is unlikely to confound Infinium 450K methylation analysis in whole blood.

dCas9-mediated Nanoelectrokinetic Direct Detection of Target Gene for Liquid Biopsy

The-state-of-the-art bio- and nanotechnology have opened up an avenue to noninvasive liquid biopsy for identifying diseases from biomolecules in bloodstream, especially DNA. In this work, we combined sequence-specific-labeling scheme using mutated clustered regularly interspaced short palindromic repeats associated protein 9 without endonuclease activity (CRISPR/dCas9) and ion concentration polarization (ICP) phenomenon as a mechanism to selectively preconcentrate targeted DNA molecules for rapid and direct detection. Theoretical analysis on ICP phenomenon figured out a critical mobility, elucidating two distinguishable concentrating behaviors near a nanojunction, a stacking and a propagating behavior. Through the modulation of the critical mobility to shift those behaviors, the C-C chemokine receptor type 5 ( CCR5) sequences were optically detected without PCR amplification. Conclusively, the proposed dCas9-mediated genetic detection methodology based on ICP would provide rapid and accurate micro/nanofluidic platform of liquid biopsies for disease diagnostics.

Extraction of electrokinetically separated analytes with on-demand encapsulation

Microchip electrokinetic methods are capable of increasing the sensitivity of molecular assays by enriching and purifying target analytes. However, their use is currently limited to assays that can be performed under a high external electric field, as spatial separation and focusing is lost when the electric field is removed. We present a novel method that uses two-phase encapsulation to overcome this limitation. The method uses passive filling and pinning of an oil phase in hydrophobic channels to encapsulate electrokinetically separated and focused analytes with a brief pressure pulse. The resulting encapsulated sample droplet maintains its concentration over long periods of time without requiring an electric field and can be manipulated for further analysis, either on- or off-chip. We demonstrate the method by encapsulating DNA oligonucleotides in a 240 pL aqueous segment after isotachophoresis (ITP) focusing, and show that the concentration remains at 60% of the initial value for tens of minutes, a 22-fold increase over free diffusion after 20 minutes. Furthermore, we demonstrate manipulation of a single droplet by selectively encapsulating amplicon after ITP purification from a polymerase chain reaction (PCR) mix, and performing parallel off-chip detection reactions using the droplet. We provide geometrical design guidelines for devices implementing the encapsulation method, and show how the method can be scaled to multiple analyte zones.

Poly-adenine-mediated spherical nucleic acids for strand displacement-based DNA/RNA detection

DNA-gold nanoparticles (AuNPs) conjugate is one of the most versatile bionanomaterials for biomedical and clinical diagnosis. However, to finely tune the hybridization ability and precisely control the orientation and conformation of surface-tethered oligonucleotides on AuNPs remains a hurdle. In this work, we developed a poly adenine-mediated spherical nucleic acid (polyA-mediated SNA) strategy by assembling di-block DNA probes on gold nanoparticles (AuNPs) to spatially control interdistance and hybridization ability of oligonucleotides on AuNPs. By modulating length of poly A bound on the SNA with different degrees of constructing, we presented significant improved biosensing performance including high hybridization efficiency, and expanded dynamic range of analytes with more sensitive detection limit. Furthermore, this polyA design could facilitate the programmable detection for DNA in serum environment and simultaneous multicolor detection of three different microRNAs associated with pancreatic carcinoma. The demonstration of the link between modulation of SNA assembly strategy and biodetection capability will increase the development of high performance diagnostic tools for translational biomedicine.

Extraction of Genomic DNA via Superparamagnetic Fe₃O₄ Magnetic Colloidal Nanocrystal Clusters

We herein describe a solvothermal method for preparing superparamagnetic Fe3O4 magnetic colloidal nanocrystal clusters with an average diameter of 195 nm. The Fe3O4 magnetic colloidal nanocrystal clusters were characterized by transmission electron microscopy (TEM), dynamic light scattering (DLS) and other methods. The Fe3O4 magnetic colloidal nanocrystal clusters were used to extract genomic DNA from fresh blood, Gram-negative bacteria, Gram-positive bacteria and frozen blood. Results showed that the genomic DNA integrity, purity and yield extracted via this universal method were satisfactory. This method is rapid, simple and does not use protease K or toxic compounds. This method lays the foundation for future research and nucleic acid extraction techniques.

Do bednets including piperonyl butoxide offer additional protection against populations of Anopheles gambiae s.l. that are highly resistant to pyrethroids? An experimental hut evaluation in Burkina Fasov

Malaria control is dependent on the use of longlasting insecticidal nets (LLINs) containing pyrethroids. A new generation of LLINs containing both pyrethroids and the synergist piperonyl butoxide (PBO) has been developed in response to increasing pyrethroid resistance in African malaria vectors, but questions remain about the performance of these nets in areas where levels of pyrethroid resistance are very high. This study was conducted in two settings in southwest Burkina Faso, Vallée du Kou 5 and Tengrela, where Anopheles gambiae s.l. (Diptera: Culicidae) mortality rates in World Health Organization (WHO) discriminating dose assays were < 14% for permethrin and < 33% for deltamethrin. When mosquitoes were pre-exposed to PBO in WHO tube assays, mortality rates increased substantially but full susceptibility was not restored. Molecular characterization revealed high levels of kdr alleles and elevated levels of P450s previously implicated in pyrethroid resistance. In cone bioassays and experimental huts, PBO LLINs outperformed the pyrethroid-only equivalents from the same manufacturers. Blood feeding rates were 1.6-2.2-fold lower and mortality rates were 1.69-1.78-fold greater in huts with PBO LLINs vs. non-PBO LLINs. This study indicates that PBO LLINs provide greater personal and community-level protection than standard LLINs against highly pyrethroid-resistant mosquito populations.

Improving the Performance of DNA Strand Displacement Circuits by Shadow Cancellation

DNA strand displacement circuits are powerful tools that can be rationally engineered to implement molecular computing tasks because they are programmable, cheap, robust, and predictable. A key feature of these circuits is the use of catalytic gates to amplify signal. Catalytic gates tend to leak; that is, they generate output signal even in the absence of intended input. Leaks are harmful to the performance and correct operation of DNA strand displacement circuits. Here, we present "shadow cancellation", a general-purpose technique to mitigate leak in catalytic DNA strand displacement circuits. Shadow cancellation involves constructing a parallel shadow circuit that mimics the primary circuit and has the same leak characteristics. It is situated in the same test tube as the primary circuit and produces "anti-background" DNA strands that cancel "background" DNA strands produced by leak. We demonstrate the feasibility and strength of the shadow leak cancellation approach through a challenging test case, a cross-catalytic feedback DNA amplifier circuit that leaks prodigiously. Shadow cancellation dramatically reduced the leak of this circuit and improved the signal-to-background difference by several fold. Unlike existing techniques, it makes no modifications to the underlying amplifier circuit and is agnostic to its leak mechanism. Shadow cancellation also showed good robustness to concentration errors in multiple scenarios. This work introduces a direction in leak reduction techniques for DNA strand displacement amplifier circuits and can potentially be extended to other molecular amplifiers.

Synthesis of Chiral Carbo-Nanotweezers for Enantiospecific Recognition and DNA Duplex Winding in Cancer Cells

Targeting the DNA of tumor cells with small molecules may offer effective clinical strategies for transcriptional inhibition. We unveil synthesis and characterization of ∼20 nm chiral carbon nanoparticles for enantiospecific recognition of DNA. Our approach inculcates chirality in carbon nanoparticles by controlled tethering of minor groove binders, i.e., Tröger's base (TB). The chiral particles positively enriched the cellular nucleus in MCF-7 breast cancer cells, irrespective of the TB asymmetry tethered on the particle surface, but negatively induced chiral carbon nanoparticles exhibited improved efficiency at inhibiting cell growth. Further studies indicated that these chiral particles act as nanotweezers to perturb the genomic DNA and induce apoptosis cascade in cancer cells.

DNA on feminine sanitary products

The use of feminine hygiene products is commonplace and chaperones many women for most of their reproductive years. Unless specifically labelled, products are usually not sterile. Any DNA present on their surface could potentially be transferred onto the wearer and subsequently be detected in samples taken from intimate areas during a medical examination. This study investigated whether unused feminine sanitary products normally carry detectable amounts of DNA. Altogether, 52 items of tampons, pads, liners, and wipes were tape lifted and subjected to total and male-specific DNA quantification and STR amplification. Nineteen of these returned quantification values greater than zero. However, only four (one tampon and three liners) displayed one or two Y-STRs, whereas one pad exhibited one autosomal allele and an amelogenin X allele. All peak heights were below 515 RFU. Two liners may have collected partner DNA post purchase since they were not individually wrapped. Thus, feminine sanitary products are normally not a source of DNA.

Optimization of DNA isolation method from Formalin-Fixed-Paraffin-Embedded tissues (FFPE) and comparative performance of four different Polymerase Chain Reaction (PCR) kits

The tissue sample may have important genetic information in diagnostic, prognostic and counselling issues. Formalin-Fixed-Paraffin-Embedded (FFPE) is a routine method for preserving tissues. However, DNA isolated from FFPE tissue is often difficult to be amplified in PCR due to fragmentation and DNA-protein crosslinks. This study aimed to optimize the DNA isolation method from FFPE tissue and compare the performance of four different PCR ready-to-use kits. Genomic DNA was isolated from FFPE tissue colon of Short-segment Hirschsprung (S-HSCR) patients and prostate cancer tissue using Quick-DNA™ FFPE Kit (Zymo Research) with and without pre-heating treatment in KOH/NOH solution. Primers for Androgen Receptor (AR) gene and four different PCR kits: MyTaq HS Red Mix 2X (BioLine), FastStart Taq DNA Polymerase (Roche), KAPA2G fast PCR Kit 2X (KAPA Biosystem) and KOD FX Neo (Toyobo) were used for amplification. DNA electrophoresis was performed to compare the PCR results. BioLine and Toyobo kits gave better PCR results than those of Roche and KAPA Biosystem. Increasing amount of Taq polymerase and dNTPs of Roche kit by two-fold could increase the quality of PCR results. Toyobo could amplify DNA up to 417 bp, however, none of these PCR kits could amplify DNA above 450 bp. Pre-heated treatment of FFPE tissue in NaOH/KOH did not improve the DNA quality and PCR results. Toyobo PCR ready-to-use kit gave the best result among the other three PCR kits used in this study in amplifying DNA isolated from FFPE tissue. Designing the primers producing amplicon not more than 450 bp is suggested.

Alkylamine ion-pairing reagents and the chromatographic separation of oligonucleotides

Alkylamines are commonly used to improve both chromatographic and mass spectral performance of electrospray ionization liquid chromatography mass spectrometry based methods for the analysis of oligonucleotides. Recently several new alkylamines have been introduced to enhance the electrospray mass spectral response for oligonucleotides; however, the chromatographic properties of these new alkylamines have not been rigorously assessed. We have investigated the retention, peak width, resolution and general chromatographic performance of fifteen different alkylamines for the separation of a model DNA, RNA and an antisense therapeutic oligonucleotide. Eleven of the fifteen alkylamines were shown to provide similar chromatographic performance across all three classes of oligonucleotides. Based on these findings, a model for the mechanism of retention of oligonucleotides using alkylamines and hexafluoroisopropanol mobile phases is proposed. Depending on the concentrations of alkylamines and pH adjustment, oligonucleotides can be retained by micellar chromatography and not the generally held ion-pairing mechanism. This conclusion is supported by light scattering, transmission electron microscopy and ion mobility experiments detecting three micron aggregates in the mobile phase at concentrations that are routinely used for LC-MS analysis of oligonucleotides. These aggregates are not detected at lower alkylamine concentrations where the retention mechanism follows an ion-pairing mechanism. The formation of these aggregates appears to be dependent on the pH of the mobile phase.

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

Modern genotyping techniques, such as SNP analysis and genotyping by sequencing (GBS), are hampered by poor DNA quality and purity, particularly in challenging plant species, rich in secondary metabolites. We therefore investigated the utility of a pre-wash step using a buffered sorbitol solution, prior to DNA extraction using a high salt CTAB extraction protocol, in a high throughput or miniprep setting. This pre-wash appears to remove interfering metabolites, such as polyphenols and polysaccharides, from tissue macerates. We also investigated the adaptability of the sorbitol pre-wash for RNA extraction using a lithium chloride-based protocol. The method was successfully applied to a variety of tissues, including leaf, cambium and fruit of diverse plant species including annual crops, forest and fruit trees, herbarium leaf material and lyophilized fungal mycelium. We consistently obtained good yields of high purity DNA or RNA in all species tested. The protocol has been validated for thousands of DNA samples by generating high data quality in dense SNP arrays. DNA extracted from Eucalyptus spp. leaf and cambium as well as mycelium from Trichoderma spp. was readily digested with restriction enzymes and performed consistently in AFLP assays. Scaled-up DNA extractions were also suitable for long read sequencing. Successful RNA quality control and good RNA-Seq data for Eucalyptus and cashew confirms the effectiveness of the sorbitol buffer pre-wash for high quality RNA extraction.

Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores

Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the CRISPR-dCas9 variant employed here does not cut DNA but instead remains tightly bound at a user-defined binding site, thus providing an excellent target for biosensing. In our nanopore experiments, we observe the CRISPR-dCas9 proteins as local spikes that appear on top of the ionic current blockade signal of DNA molecules that translocate through the nanopore. The proteins exhibit a pronounced blockade signal that allows for facile identification of the targeted sequence. Even at the high salt conditions (1 M LiCl) required for nanopore experiments, dCas9 proteins are found to remain stably bound. The binding position of the target sequence can be read from the spike position along the DNA signal. We anticipate applications of this nanopore-based CRISPR-dCas9 biosensing approach in DNA-typing based diagnostics such as quick disease-strain identification, antibiotic-resistance detection, and genome typing.

Comparative Study of Five Commercially Available Saliva Collection Kits for DNA Extraction

BACKGROUND

Obtaining DNA samples through saliva samples is becoming more common, and more companies are responding to this demand with saliva collection/DNA extraction kits.

METHODS

The University of Pittsburgh's School of Dental Medicine maintains a DNA bank, which our lab helps direct. While we have always used Oragene (DNAGenotek, Kanata, Canada) kits to collect samples in the past, we recently compared 5 alternative kits/methods in an effort to reduce costs while maintaining quality. The kits/ methods were: Norgen (Norgen Biotek Corp., Thorold, Canada), Stratec (Stratec Biomedical, Birkenfeld, Germany), DNAgard (Biomatrica, San Diego, CA, USA), Oasis (Oasis Diagnostics, Vancouver, WA, USA), and an inhouse protocol for DNA extraction from whole saliva. We compared 7 protocols for extracting DNA from saliva using 5 commercially available kits. We primarily looked at total DNA yield, but also considered cost, ease of sample collection, and complexity of extraction protocol.

RESULTS

When compared to the Oragene kits, only Norgen and Startec had comparable DNA yields (30 µg or more). Oasis was the easiest to use in terms of sample collection.

CONCLUSIONS

When compared to our whole saliva DNA extraction protocol, all kits had higher yields, shorter extraction time, and easier protocols.

Pressure-Modulated Selective Electrokinetic Trapping for Direct Enrichment, Purification, and Detection of Nucleic Acids in Human Serum

Micro total-analysis systems (μTAS) have been extensively developed for the detection of nucleic acids (NAs) in resource-limited settings in recent years, yet the sample-preparation steps that interface real-world samples with on-chip analytics remain as the technical bottleneck. We report pressure-modulated selective electrokinetic trapping (PM-SET) for the direct enrichment, purification, and detection of NAs in human serum in one step without involving tedious solid-phase extraction, chemical amplification, and surface-hybridization-based assays. Under appropriately modulated hydrostatic pressures, NAs in human serum were selectively enriched in an electrokinetic concentrator with the majority of background proteins removed, achieving an enrichment factor of >4800 in 15 min. A sequence-specific NA was detected simultaneously during the enrichment process using a complementary morpholino (MO) probe, realizing a limit of detection of 3 pM in 15 min. PM-SET greatly reduces the cost, time, and complexity of sample preparation for NA detection and could be easily interfaced with existing NA-detection devices to achieve true sample-to-answer biomolecular analytics.

Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata

Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.

A simplified and optimized protocol for total DNA extraction from insect species: applicable for studying genetic diversity and PCR-based specimen identification via partial amplification of cytochrome oxidase I (COI) gene

The efficient DNA extraction from insects has been suggested as a critical and main step affecting molecular entomology for taxonomic identification, the establishment of DNA barcoding library and analysis of genetic diversity relationship between insect populations. For successfully apply these molecular techniques, high-quantity and high-quality of the extracted DNA are required. Several protocols for efficient genomic DNA extraction from insects have been developed. In this research, we represent a rapid, reliable and cost-effective method that it is not reliant on poisonous and enzymatic reagents for DNA extraction from insect tissues. Results showed that high quantity and high-quality of the isolated DNA by this method is suitable and can be used directly for PCR, also is enough to do hundreds of molecular reactions. In conclusion, we described a fast, cost-effective, non-toxic and enzyme-free protocol for high yield genomic DNA extraction from green Lacewings (Chrysoperla carnea) tissues in basic equipment laboratories.

Isolation and characterization of a dihydrofolate reductase gene mutation in methotrexate-resistant Drosophila cells

Stepwise increases in methotrexate (MTX) concentration over a 4-year period led to the selection of a highly drug-resistant (2 x 10(-4) M MTX) Drosophila cell line. Uptake experiments with [3H]MTX showed a slightly lower level of intracellular MTX in the resistant S3Mtx cells than in the susceptible S3 parental cell line. Southern blot analysis demonstrated that the gene for the MTX target, dihydrofolate reductase (DHFR), was not significantly amplified in the resistant line. To determine the molecular basis for resistance, the DHFR cDNA sequence was amplified by polymerase chain reaction from both the resistant and susceptible cells. Sequence comparison revealed a single T to A base change at nucleotide 89, which resulted in the substitution of Gln for Leu at residue 30 in S3Mtx cells. Expression and purification of the wild-type and mutant DHFR from E. coli cells showed that the S3Mtx enzyme had a reduced binding affinity for the antifolates, MTX and trimethoprim, with 15-fold higher K[d] and K[i] values than those from the wild-type enzyme. Molecular modeling confirmed that the replacement of the hydrophobic Leu by the more polar Gln was in the substrate binding site and thus would decrease the binding of MTX. These results suggest that the high level of MTX resistance in the selected cell line can be attributed to the mutation in the DHFR gene and also provides a model for pesticide resistance in insects.

Short-Length DNA Adsorption on Graphene Oxide-Coated Microbeads for DNA Target Separation from Clinical Samples

Nucleic acid preparation (concentration and purification of various nucleic acid targets) from biological samples is essential for personalized and precision medicine. The adsorption of short-length DNA on graphene oxide (GO) layers was investigated and compared with that on silica surfaces. GO was efficiently coated on glass beads to be used more easily and spatially. Surface of the GO bead was confirmed by field-emission scanning electron microscopy. GO-coated beads were packed and the adsorption conditions of short-length DNA were optimized under various pH and flow rate conditions. The amount of adsorbed DNA was confirmed by real-time polymerase chain reaction and visualized using fluorescence microscopy.

A minimum requirements method to isolate large quantities of highly purified DNA from one drop of poultry blood

Here, we describe a rapid, efficient and noncomplicated method for extracting poultry genomic DNA. This simple method obtains excellent qualities of molecular biology grade DNA in a matter of only about 15 min. A straightforward protocol is followed in this extraction procedure, in which, when the blood cells are placed in a distilled water alone, water rapidly disrupts red blood cells (RBCs) membranes and alleviate chickens' undesired high blood viscosity without being aided by any other chemicals. Moreover, the time, cost and efforts were hugely reduced since the step of leukocytes lysis was successfully mixed with the protein precipitation. The isolated genomic DNA, in terms of its quantity and quality, is satisfying and is proved to be suitable for restriction endonucleases digestion, polymerase chain reaction (PCR), and restriction fragment length polymorphism (RFLP). Thus, instead of extracting a limited amount of DNA using expensive or relatively expensive kits, this guaranteed procedure can be utilized alternatively to accurately extract genomic DNA (gDNA) from minimal starter quantities of the chicken's blood that do not exceed 50 μL. By relying on this technique, all the practical handover steps are reduced to the extreme limits. This pilot study may provide a high yield gDNA extraction that minimizes labour, expense, and steps in very high competency and reproducibility.

Ampholytic ion-exchange materials coated with small zwitterions for high-efficacy purification of ionizable soluble biomacromolecules

For the purification of soluble proteins and nucleic acids through ion-exchange, the ampholytic ion-exchange materials (AIEMs) were designed, which possessed both short aliphatic carboxyl and short aliphatic amines/imidazole at optimized ratios on solid supports coated with high density of small zwitterions; under optimized conditions, the soluble ionizable biomacromolecules were adsorbed on those AIEMs via electrostatic attractions and eluted effectively through electrostatic repulsions. As the proof-of-concept, magnetic submicron particles bearing short aliphatic carboxyl and the coats of small zwitterion served as the starting solid supports, which were conjugated with lysine alone, or with lysine plus glycine or N,N‑dimethylethylenediamine, to yield magnetic AIEMs whose surfaces possessed zero net charges at different pH. Such magnetic AIEMs exhibited ideal efficacy to release acid red 13 as an anion at the elution pH optimized for strong electrostatic repulsions; those magnetic AIEMs were proven absorbing under optimized conditions for the purification of soluble proteins stable at pH close to their isoelectric points and solid-phase extraction of nucleic acids in applicable biological mixtures. Therefore, the designed AIEMs are promising for the high-efficacy purification of ionizable soluble biomacromolecules.

Molecular organization of the rat glia-derived nexin/protease nexin-1 promoter

The first three exons and the promoter of rat glia-derived nexin, also called protease nexin-1 (GDN/PN-1), have been identified through analysis of rat genomic clones. A 1.6 kilobase (kb) fragment containing 105 base pairs of the first exon and 5'-flanking sequences was sequenced. The 5'-flanking sequence and the first exon were found to be GC-rich, indicating that the 5' region of the rat GDN/PN-1 gene resides within a CpG island. A TATA box-like sequence, but no CAAT box, was found. The rat GDN/PN-1 promoter contains five SP1 consensus sites, four consensus sites for the MyoD1 transcription factor, and one binding site for the transcription factors NGFI-A, NGFI-C, Krox-20, and Wilms tumor factor. The presence of these consensus sequences is consistent with the known expression pattern of GDN/PN-1. Primer extension and RNase protection assays identified one transcriptional start site. The 1.6 kb promoter fragment cloned in a reporter plasmid was found to induce firefly luciferase expression in a cell-specific manner. A positive regulatory element is localized in the region -1545 to -389. In vitro CpG methylation blocked transcription from the GDN/PN-1 promoter in rat hepatoma cells but not in C6 rat glioma cells.

NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids

Selective extraction of a small amount of nucleic acids from complex biological samples containing a high concentration of proteins is critical for bioanalytical chemistry. A number of previously published studies have focused on long, double-stranded DNA such as plasmid DNA. On the other hand, we are interested in short oligonucleotides. Nucleic acids have a negatively charged phosphate backbone that interacts with metal oxides strongly, and this may be used to distinguish them from proteins. In this work, a few metal oxide nanoparticles were screened, including NiO, CoO, ZnO, TiO₂, CeO₂, and Fe₃O₄ for DNA recovery. NiO had the highest DNA adsorption efficiency from mixtures containing bovine serum albumin or human blood serum. The adsorption of DNA by NiO was further characterized as a function of the pH, salt concentration, DNA length, and DNA sequence. The adsorption mechanism was studied by adding competing chemicals or denaturing agents. A striking observation was the extremely high adsorption affinity of NiO, much higher than that of the other tested oxides. Polyphosphate was the most effective agent for displacing adsorbed DNA, whereas simple inorganic phosphate was less effective. NiO was able to concentrate DNA from a serum mixture by 33- to 55-fold, depending on the serum concentration. NiO is thus a promising candidate for extracting DNA from biological samples.

Long-term stability and computational analysis of migration patterns of L-MYC immortalized neural stem cells in the brain

Background

Preclinical studies indicate that neural stem cells (NSCs) can limit or reverse central nervous system (CNS) damage through delivery of therapeutic agents for cell regeneration. Clinical translation of cell-based therapies raises concerns about long-term stability, differentiation and fate, and absence of tumorigenicity of these cells, as well as manufacturing time required to produce therapeutic cells in quantities sufficient for clinical use. Allogeneic NSC lines are in growing demand due to challenges inherent in using autologous stem cells, including production costs that limit availability to patients.

Methods/Principal findings

We demonstrate the long-term stability of L-MYC immortalized human NSCs (LM-NSC008) cells in vivo, including engraftment, migration, and absence of tumorigenicity in mouse brains for up to nine months. We also examined the distributions of engrafted LM-NSC008 cells within brain, and present computational techniques to analyze NSC migration characteristics in relation to intrinsic brain structures.

Conclusions/Significance

This computational analysis of NSC distributions following implantation provides proof-of-concept for the development of computational models that can be used clinically to predict NSC migration paths in patients. Previously, models of preferential migration of malignant tumor cells along white matter tracts have been used to predict their final distributions. We suggest that quantitative measures of tissue orientation and white matter tracts determined from MR images can be used in a diffusion tensor imaging tractography-like approach to describe the most likely migration routes and final distributions of NSCs administered in a clinical setting. Such a model could be very useful in choosing the optimal anatomical locations for NSC administration to patients to achieve maximum therapeutic effects.

Generation of ChIP-Loop Libraries

The ChIP-loop method combines the standard 3C protocol with a routine ChIP protocol. This method allows the selective identification of long-range chromatin interactions between loci that are bound to specific proteins of interest. ChIP-loop experiments need to be designed and planned as described for the standard 3C protocol. First, identify a restriction enzyme that digests chromatin so that the elements of interest are located on separate restriction fragments. Second, determine whether an antibody is available that successfully immunoprecipitates the protein of interest in a typical ChIP experiment.

The changing views on the evolutionary relationships of extant Salamandridae (Amphibia: Urodela)

The phylogenetic relationships among members of the family Salamandridae have been repeatedly investigated over the last 90 years, with changing character and taxon sampling. We review the changing composition and the phylogenetic position of salamandrid genera and species groups and add a new phylogeny based exclusively on sequences of nuclear genes. Salamandrina often changed its position depending on the characters used. It was included several times in a clade together with the primitive newts (Echinotriton, Pleurodeles, Tylototriton) due to their seemingly ancestral morphology. The latter were often inferred as a monophyletic clade. Respective monophyly was almost consistently established in all molecular studies for true salamanders (Chioglossa, Lyciasalamandra, Mertensiella, Salamandra), modern Asian newts (Cynops, Laotriton, Pachytriton, Paramesotriton) and modern New World newts (Notophthalmus, Taricha). Reciprocal non-monophyly has been established through molecular studies for the European mountain newts (Calotriton, Euproctus) and the modern European newts (Ichthyosaura, Lissotriton, Neurergus, Ommatotriton, Triturus) since Calotriton was identified as the sister lineage of Triturus. In pre-molecular studies, their respective monophyly had almost always been assumed, mainly because a complex courtship behaviour shared by their respective members. Our nuclear tree is nearly identical to a mito-genomic tree, with all but one node being highly supported. The major difference concerns the position of Calotriton, which is no longer nested within the modern European newts. This has implications for the evolution of courtship behaviour of European newts. Within modern European newts, Ichthyosaura and Lissotriton changed their position compared to the mito-genomic tree. Previous molecular trees based on seemingly large nuclear data sets, but analysed together with mitochondrial data, did not reveal monophyly of modern European newts since taxon sampling and nuclear gene coverage was too poor to obtain conclusive results. We therefore conclude that mitochondrial and nuclear data should be analysed on their own.

Extracellular DNA in natural environments: features, relevance and applications

Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.

Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog

BACKGROUND

Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe.

RESULTS

Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs.

CONCLUSIONS

In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.

Multi-Snapshot Imaging for Chromatographic Peak Analysis

OBJECTIVE

Snapshot imaging has several advantages in automated gel electrophoresis compared with the finish-line method in capillary electrophoresis; this comes at the expense of resolution. A novel signal processing algorithm is proposed enabling a multisnapshot imaging (MSI) modality whose objective is to substantially improve resolution. MSI takes multiple-captures in time as macromolecules are electrophoresed. Peaks from latter snapshots have high resolution, but low signal-to-noise ratio (SNR), while earlier snapshots have low resolution, but high SNR.

METHODS

Signals at different capture-times are related by a scale-in-separation, shift-in-separation, and amplitude gain. The proposed method realigns the multiple captures using least-squares and fuses them. The algorithm accounts for the partial waveforms observed as the chromatic peaks exit the sensor's field-of-view.

RESULTS

MSI improves resolution by approximately [Formula: see text] on average per minute of additional electrophoresis.

CONCLUSIONS

Comprehensive analysis of the resolution quantified on several data sets demonstrates the effectiveness of MSI.

SIGNIFICANCE

MSI can double the resolution compared with traditional snap-shot imaging over a typical set of captures.

Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus)

In many human-altered ecosystems, organisms are increasingly faced with more diverse and complex environmental stressors and pollutant mixtures, to which the adaptations necessary to survive exposure are likely to be numerous and varied. Improving our understanding of the molecular mechanisms that underlie complex polygenic adaptations in natural settings requires significant toxicological, biochemical, physiological, and genomic data rarely available for non-model organisms. Here, we build upon two decades of study of adaptation to anthropogenic pollutants in a population of Atlantic killifish (Fundulus heteroclitus) that inhabits the creosote-contaminated Atlantic Wood Industries Superfund (AW) site on the Elizabeth River, Virginia in the United States. To better understand the genotypes that underlie previously characterized resistance to PCBs and PAHs, we performed Restriction site-Associated DNA sequencing (RADseq) on killifish from AW and two relatively clean reference sites (King's Creek-KC, and Mains Creek-MC). Across the genome, we analyzed over 83,000 loci and 12,000 single nucleotide polymorphisms (SNPs). Shared across both comparisons of killifish from polluted (AW) and relatively unpolluted (KC and MC) sites, we found eight genomic regions with smoothed FST values significantly (p < 0.001) elevated above background. Using the recently published F. heteroclitus reference genome, we identified candidate genes in these significant regions involved in the AHR pathway (e.g. AIP, ARNT1c), as well as genes relating to cardiac structure and function. These genes represent both previously characterized and potentially novel molecular adaptations involved with various aspects of resistance to these environmental toxins.

The first successful application of preimplantation genetic diagnosis for hearing loss in Iran

Hearing impairment (HI) caused by mutations in the connexin-26 gene (GJB2) accounts for the majority of cases with inherited, nonsyndromic sensorineural hearing loss. Due to the illegality of the abortion of deaf fetuses in Islamic countries, preimplantation genetic diagnosis (PGD) is a possible solution for afflicted families to have a healthy offspring. This study describes the first use of PGD for GJB2 associated non-syndromic deafness in Iran. GJB2 donor splicing site IVS1+1G&gt;A mutation analysis was performed using Sanger sequencing for a total of 71 Iranian families with at least 1 deaf child diagnosed with non-syndromic deafness. In Vitro Fertilization (IVF) was performed, followed by PGD for a cousin couple with a 50% chance of having an affected child. Bi-allelic pathogenic mutations were found in a total of 12 families (~17 %); of which a couple was a PGD volunteer. The deaf woman in this family was homozygous and her husband was a carrier of the IVS1+1G&gt;A gene mutation. Among 8 biopsied embryos, two healthy embryos were implanted which resulted in a single pregnancy and subsequent birth of a healthy baby boy. This is the first report of a successful application of PGD for hearing loss in Iran. Having a baby with a severe hearing impairment often imposes families with long-term disease burden and heavy therapy costs. Today PGD has provided an opportunity for high-risk individuals to avoid the birth of a deaf child.

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

Zebrafish (Danio rerio) possess orthologues for 84% of the genes known to be associated with human diseases. In addition, these animals have a short generation time, are easy to handle, display a high reproductive rate, low cost, and are easily amenable to genetic manipulations by microinjection of DNA in embryos. Recent advances in gene editing tools are enabling precise introduction of mutations and transgenes in zebrafish. Disease modeling in zebrafish often leads to larval phenotypes and early death which can be challenging to interpret if genotypes are unknown. This early identification of genotypes is also needed in experiments requiring sample pooling, such as in gene expression or mass spectrometry studies. However, extensive genotypic screening is limited by traditional methods, which in most labs are performed only on adult zebrafish or in postmortem larvae. We addressed this problem by adapting a method for the isolation of PCR-ready genomic DNA from live zebrafish larvae that can be achieved as early as 72 h post-fertilization (hpf). This time and cost-effective technique, improved from a previously published genotyping protocol, allows the identification of genotypes from microscopic fin biopsies. The fins quickly regenerate as the larvae develop. Researchers are then able to select and raise the desired genotypes to adulthood by utilizing this high-throughput PCR-based genotyping procedure.

Modeling of DNA transport in viscoelastic electro-hydrodynamic flows for enhanced size separation

DNA separation and analysis have advanced over recent years, benefiting from microfluidic systems that reduce sample volumes and analysis costs, essential for sequencing and disease identification in body fluids. We recently developed the μLAS technology that enables the separation, concentration, and analysis of nucleic acids with high sensitivity. The technology combines a hydrodynamic flow actuation and an opposite electrophoretic force in viscoelastic polymer solutions. Combining hydrodynamics first principles and statistical mechanics, we provide, in this paper, a quantitative model of DNA transport capable of predicting device performance with the exclusive use of one adjustable parameter associated with the amplitude of transverse viscoelastic forces. The model proves to be in remarkable agreement with DNA separation experiments, and allows us to define optimal conditions that result in a maximal resolution length of 7 bp. We finally discuss the usefulness of our model for separation technologies involving viscoelastic liquids.

MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT

DNA methylation is the most characterized epigenetic process exhibiting stochastic variation across different tissues and individuals. In non-invasive prenatal testing (NIPT) fetal specific methylated regions can potentially be used as biomarkers for the accurate detection of fetal aneuploidies. The aim of this study was the investigation of inter-individual methylation variability of previously reported fetal-specific markers and their implementation towards the development of a novel NIPT assay for the detection of trisomies 13, 18, and 21. Methylated DNA Immunoprecipitation (MeDIP) combined with in-solution targeted enrichment followed by NGS was performed in 29 CVS and 27 female plasma samples to assess inter-individual methylation variability of 331 fetal-specific differentially methylated regions (DMRs). The same approach was implemented for the NIPT of trisomies 13, 18 and 21 using spiked-in (n = 6) and pregnancy samples (n = 44), including one trisomy 13, one trisomy 18 and four trisomy 21. Despite the variability of DMRs, CVS samples showed statistically significant hypermethylation (p<2e-16) compared to plasma samples. Importantly, our assay correctly classified all euploid and aneuploid cases without any false positive results (n = 44). This work provides the starting point for the development of a NIPT assay based on a robust set of fetal specific biomarkers for the detection of fetal aneuploidies. Furthermore, the assay’s targeted nature significantly reduces the analysis cost per sample while providing high read depth at regions of interest increasing significantly its accuracy.

Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing

Ribonucleotides embedded within DNA render the DNA sensitive to the formation of single-stranded breaks under alkali conditions. Here, we describe a next-generation sequencing method called hydrolytic end sequencing (HydEn-seq) to map ribonucleotides inserted into the genome of Saccharomyce cerevisiae strains deficient in ribonucleotide excision repair. We use this method to map several genomic features in wild-type and replicase variant yeast strains.

Constructing Smart Protocells with Built-In DNA Computational Core to Eliminate Exogenous Challenge

A DNA reaction network is like a biological algorithm that can respond to "molecular input signals", such as biological molecules, while the artificial cell is like a microrobot whose function is powered by the encapsulated DNA reaction network. In this work, we describe the feasibility of using a DNA reaction network as the computational core of a protocell, which will perform an artificial immune response in a concise way to eliminate a mimicked pathogenic challenge. Such a DNA reaction network (RN)-powered protocell can realize the connection of logical computation and biological recognition due to the natural programmability and biological properties of DNA. Thus, the biological input molecules can be easily involved in the molecular computation and the computation process can be spatially isolated and protected by artificial bilayer membrane. We believe the strategy proposed in the current paper, i.e., using DNA RN to power artificial cells, will lay the groundwork for understanding the basic design principles of DNA algorithm-based nanodevices which will, in turn, inspire the construction of artificial cells, or protocells, that will find a place in future biomedical research.

[Application of Touch DNA in Investigation Practice]

With the continuous development of DNA extraction and testing technology, the DNA left at a crime scene plays a decisive role in the determination of criminal suspects in criminal investigation. But in the meanwhile, the anti-reconnaissance awareness of suspect is growing, which leads to a decrease of evidence left at scene during and after a crime. Therefore, in the process of evidence collection at scene, the finding and extraction of touch biological evidence, and the DNA detection are more and more important. At present, the proportion of touch evidence at the crime scene increases, which plays an increasingly important role in the detection of cases. However, with the characteristics of minute quantities, small size and secrecy, these touch evidence is difficult to be observed. What's more, various forms of pollution at the scene greatly accelerate the degradation rate of trace material, thus, the test and analysis of such material has become the emphasis and difficulty of the forensic evidence identification. This article reviews different kinds, collection and extraction methods of touch DNA, the factors that affect the detection and the problems may meet in the detection for providing an application prospect to the forensic practice.