DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis

Engineering in vitro models of cystic fibrosis lung disease using neutrophil extracellular trap inspired biomaterials

Cystic fibrosis (CF) is a muco-obstructive lung disease where inflammatory responses due to chronic infection result in the accumulation of neutrophil extracellular traps (NETs) in the airways. NETs are web-like complexes comprised mainly of decondensed chromatin that function to capture and kill bacteria. Prior studies have established excess release of NETs in CF airways increases viscoelasticity of mucus secretions and reduces mucociliary clearance. Despite the pivotal role of NETs in CF disease pathogenesis, current in vitro models of this disease do not account for their contribution. Motivated by this, we developed a new approach to study the pathobiological effects of NETs in CF by combining synthetic NET-like biomaterials, composed of DNA and histones, with an in vitro human airway epithelial cell culture model. To determine the impact of synthetic NETs on airway clearance function, we incorporated synthetic NETs into mucin hydrogels and cell culture derived airway mucus to assess their rheological and transport properties. We found that the addition of synthetic NETs significantly increases mucin hydrogel and native mucus viscoelasticity. As a result, mucociliary transport in vitro was significantly reduced with the addition of mucus containing synthetic NETs. Given the prevalence of bacterial infection in the CF lung, we also evaluated the growth of Pseudomonas aeruginosa in mucus with or without synthetic NETs. We found mucus containing synthetic NETs promoted microcolony growth and prolonged bacterial survival. Together, this work establishes a new biomaterial enabled approach to study innate immunity mediated airway dysfunction in CF.

Adipocyte "Fatty Acid Binding Protein" Gene Polymorphisms (rs1054135, rs16909196 and rs16909187) in Jordanians with Obesity and Type 2 Diabetes Mellitus

Background

Obesity, type 2 diabetes mellitus (T2DM), and dyslipidemia may result from the interactions of genetic and environmental factors. There are controversial reports concerning the association of polymorphisms (rs1054135, rs16909196 and rs16909187) in the gene of adipocyte fatty acid binding protein (FABP4) with obesity and T2DM. Therefore, we designed this study to determine the association of these polymorphisms with obesity, T2DM, and dyslipidemia among Jordanian subjects.

Methods

The study was approved by the National Center for Diabetes, Endocrinology, and Genetics (NCDEG) Institutional Review Board (IRB). A total of 397 subjects were enrolled in the study and divided into four groups as described in materials and methods section. The fatty acid binding protein 4 (FABP4) gene containing (rs1054135, rs16909196 and rs16909187) single nucleotide polymorphisms (SNP) was amplified by polymerase chain reaction (PCR) followed by Sanger DNA sequencing of the PCR product.

Results

None of the three SNPs were associated with T2DM (p > 0.05). The rs16909187 and rs16909196 were significantly associated with obesity. The wild type (CC) of rs16909187 was significantly higher among the overweight and obese group compared with normal weight controls (OD = 2.17, 95% CI = 1.18 - 3.96, p =0.01). The wild type of rs16909196 (AA) was significantly higher among the overweight and obese group compared to controls, (OD = 2.26, 95% CI = 1.24 - 4.14, p = 0.01). These results may indicate that the wild-type may be a risk factor for obesity.Only the rs1054135 SNP was significantly associated with increased low density lipoprotein (LDL) levels in the overweight and obese group compared with the controls (p = 0.03).

Conclusions

The wild-type genotypes of rs16909196 and rs16909187 may be risk factors for obesity but not T2DM. None of the three SNPs was associated with T2DM.

The Effect of Supplementation with Betaine and Zinc on In Vitro Large Intestinal Fermentation in Iberian Pigs under Heat Stress

We investigated the effects of betaine and zinc on the in vitro fermentation of pigs under heat stress (HS). Twenty-four Iberian pigs (43.4 ± 1.2 kg) under HS (30 °C) were assigned to treatments for 4 weeks: control (unsupplemented), betaine (5 g/kg), and zinc (0.120 g/kg) supplemented diet. Rectal content was used as the inoculum in 24-hincubations with pure substrates (starch, pectin, inulin, cellulose). Total gas, short-chain fatty acid (SCFA), and methane production and ammonia concentration were measured. The abundance of total bacteria and several bacterial groups was assessed. Betaine increased the acetate production with pectin and inulin, butyrate production with starch and inulin, and ammonia concentration, and decreased propionate production with pectin and inulin. The abundance of Bifidobacterium and two groups of Clostridium decreased with betaine supplementation. Zinc decreased the production of SCFA and gas with starch and inulin, associated with diminished bacterial activity. Propionate production decreased with starch, pectin, and inulin while butyrate production increased with inulin, and isoacid production increased with cellulose and inulin in pigs supplemented with zinc. The ammonia concentration increased for all substrates. The Clostridium cluster XIV abundance decreased in pigs fed zinc supplemented diets. The results reported were dependent on the substrate fermented, but the augmented butyrate production with both betaine and zinc could be of benefit for the host.

Fecal microbiota composition is related to brown adipose tissue 18F-fluorodeoxyglucose uptake in young adults

OBJECTIVE

Human brown adipose tissue (BAT) has gained considerable attention as a potential therapeutic target for obesity and its related cardiometabolic diseases; however, whether the gut microbiota might be an efficient stimulus to activate BAT metabolism remains to be ascertained. We aimed to investigate the association of fecal microbiota composition with BAT volume and activity and mean radiodensity in young adults.

METHODS

82 young adults (58 women, 21.8 ± 2.2 years old) participated in this cross-sectional study. DNA was extracted from fecal samples and 16S rRNA sequencing was performed to analyse the fecal microbiota composition. BAT was determined via a static 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography-computed tomography scan (PET/CT) after a 2 h personalized cooling protocol. 18F-FDG uptake was also quantified in white adipose tissue (WAT) and skeletal muscles.

RESULTS

The relative abundance of Akkermansia, Lachnospiraceae sp. and Ruminococcus genera was negatively correlated with BAT volume, BAT SUVmean and BAT SUVpeak (all rho ≤ - 0.232, P ≤ 0.027), whereas the relative abundance of Bifidobacterium genus was positively correlated with BAT SUVmean and BAT SUVpeak (all rho ≥ 0.262, P ≤ 0.012). On the other hand, the relative abundance of Sutterellaceae and Bifidobacteriaceae families was positively correlated with 18F-FDG uptake by WAT and skeletal muscles (all rho ≥ 0.213, P ≤ 0.042). All the analyses were adjusted for the PET/CT scan date as a proxy of seasonality.

CONCLUSION

Our results suggest that fecal microbiota composition is involved in the regulation of BAT and glucose uptake by other tissues in young adults. Further studies are needed to confirm these findings.

CLINICAL TRIAL INFORMATION

ClinicalTrials.gov no. NCT02365129 (registered 18 February 2015).

A Simplified and Efficient Method for Production of Manganese Ferrite Magnetic Nanoparticles and Their Application in DNA Isolation

A simplified, fast, and effective production method has been developed for the synthesis of manganese ferrite (MnFe₂O₄) magnetic nanoparticles (MNPs). In addition to the wide applicability of MnFe₂O₄ MNPs, this work also reports their application in DNA isolation for the first time. An ultrasonic-cavitation-assisted combustion method was applied in the synthesis of MnFe₂O₄ MNPs at different furnace temperatures (573 K, 623 K, 673 K, and 773 K) to optimize the particles' properties. It was shown that MnFe₂O₄ nanoparticles synthesized at 573 K consist of a spinel phase only with adequate size and zeta potential distributions and superparamagnetic properties. It was also demonstrated that superparamagnetic manganese ferrite nanoparticles bind DNA in buffer with a high NaCl concentration (2.5 M), and the DNA desorbs from the MNPs by decreasing the NaCl concentration of the elution buffer. This resulted in a DNA yield comparable to that of commercial DNA extraction products. Both the DNA concentration measurements and electrophoresis confirmed that a high amount of isolated bacterial plasmid DNA (pDNA) with adequate purity can be extracted with MnFe₂O₄ (573 K) nanoparticles by applying the DNA extraction method proposed in this article.

Evaluation of IL-6 and IL-17A gene polymorphisms in Iraqi patients infected with COVID-19 and type 2 diabetes mellitus

BACKGROUND

In patients with COVID-19, diabetes mellitus type 2 (T2DM) increases the risk of hospitalization and death. Patients who have IL-6 and IL-17A single nucleotide polymorphisms (SNPs) are more likely to have severe COVID-19. This study aims to determine whether SNPs of the IL-6 gene at rs1800795 (G > C) and the IL-17A gene at rs2275913 (G > A) are associated with COVID-19 and T2DM in the Iraqi population.

PATIENTS AND METHODS

Twenty-four people were divided into 4 groups as follows: six patients with severe COVID-19 and T2DM were placed in Group 1 as "G1", six patients with COVID-19 but no T2DM were placed in Group 2 as "G2", and six patients with T2DM were placed in Group 3 as "G3". There were also six healthy controls included in each group. Polymerase chain reaction (PCR) was used to amplify the target genes after genomic DNA from the blood samples was extracted. Sanger sequencing was used to find the SNPs in both the forward and reverse directions for each sample.

RESULTS

In the case of IL-6 SNP at rs1800795, the GG genotype was more common in "G3", the CC genotype was less common in all patient groups than in controls, and the GC allele was more common in "G2" than in the control group. In comparison to the controls, the three patient groups showed lower frequencies of the C allele and higher frequencies of the G allele. Regarding IL-17A gene polymorphism, the AA and GA genotypes were more prevalent in "G2" and "G3", respectively. The GG genotype and G allele frequency dropped in all patient groups compared to the control group, whereas the A allele frequency increased in all patient groups.

CONCLUSIONS

The IL-6 gene at rs1800795 (G/C) and the IL-17A gene at rs2275913 (G/A) loci were associated with COVID-19 and T2DM in Iraqi population.

Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system

BACKGROUND

The objective of the COMET (COllection of MEtabolic Tissues) biobank project is to create a high-quality collection of insulin-sensitive tissues (liver, muscle, adipose tissues, and epiploic artery) and blood sample derivatives (plasma, serum, DNA and RNA), collected from 270 grade 2-3 obese patients undergoing bariatric surgery. Relevant data on patient such as clinical/biological characteristics and sample handling are also collected. For this, our aim was to establish a Quality Management System (QMS) to meet the reliability and quality requirements necessary for its scientific exploitation.

MATERIALS AND METHODS

The COMET QMS includes: (1) Quality Assurance to standardize all stages of the biobanking process, (2) Quality Controls on samples from the first patients included in order to validate the sample management process and ensure reproducible quality; and 3) "in process" Quality Controls to ensure the reliability of the storage procedures and the stability of the samples over time.

RESULTS

For serum and plasma, several corrective actions, such as temperature handling and centrifugation conditions, were made to the protocol and led to improvement of the volume and quality of samples. Regarding DNA, all samples evaluated achieved a satisfactory level of purity and integrity and most of them yielded the required DNA quantity. All frozen tissue samples had RNAs of good purity. RNA quality was confirmed by RIN, achieving values in most cases over 7 and efficient amplification of housekeeping genes by RT-qPCR, with no significant differences among samples from the same tissue type. In the "in process" Quality Controls, DNA, RNA, and histological integrity of tissues showed no differences among samples after different preservation times.

CONCLUSION

Quality Control results have made it possible to validate the entire biobank process and confirm the utility of implementing QMS to guarantee the quality of a biospecimen collection.

Pioglitazone modulates immune activation and ameliorates inflammation induced by injured renal tubular epithelial cells via PPARγ/miRNA‑124/STAT3 signaling

Acute kidney injury (AKI) is commonly a result of renal ischemia reperfusion injury (IRI), which produces clinical complications characterized by the rapid deterioration of renal function, leading to chronic kidney disease and increases the risk of morbidity and mortality. Currently, only supportive treatment is available. AKI, which is accompanied by immune activation and inflammation, is caused by proximal tubular injury. The present study investigated the role of tubular epithelial cells as drivers of inflammation in renal IRI and their potential function as antigen-presenting cells, as well as the molecular mechanisms by which peroxisome proliferator-activated receptor-γ (PPARγ) agonists [such as pioglitazone (Pio)] exert reno-protective action in renal IRI. A total of 50 Wistar male albino rats were divided into five groups: Sham + DMSO, Sham + Pio, IRI + DMSO, IRI + prophylactic preoperative (pre) Pio and IRI + postoperative Pio. The histopathological changes in renal tissue samples and the renal epithelial cell expression of CD86, miRNA-124, STAT3, pro-inflammatory cytokines, inducible nitric oxide synthase (iNOS) and Arginase-II were analyzed by immunohistochemistry, reverse transcription-quantitative PCR, western blotting and ELISA respectively. IRI was a potent inducer for CD86 immunoexpression. An ameliorative action of Pio was demonstrated via decreased CD86 immunoexpression, upregulation of miRNA-124, decreased STAT3 expression and beneficial anti-inflammatory effects. The tubular epithelium served a notable role in the inflammatory response in renal IRI. Pio exerted its anti-inflammatory effects via PPARγ/miRNA-124/STAT3 signaling.

No Mediation Effect of Telomere Length or Mitochondrial DNA Copy Number on the Association Between Adverse Childhood Experiences (ACEs) and Central Arterial Stiffness

Background

Adverse childhood experiences (ACEs) have been linked to increased cardiovascular disease (CVD) risk. Previous reports have suggested that accelerated biological aging—indexed by telomere length (TL) and mitochondrial DNA copy number (mtDNAcn)—may contribute to associations between ACEs and cardiovascular health outcomes. Here, we examine the potential mediating effects of TL and mtDNAcn on the association between ACEs and central arterial stiffness—an intermediate cardiovascular health outcome—as a novel pathway linking ACEs to CVD risk among young adults.

Methods and Results

One hundred and eighty‐five (n=102 women; mean age, 22.5±1.5 years) individuals provided information on ACEs. TL (kb per diploid cell) and mtDNAcn (copies per diploid cell) were quantified using quantitative polymerase chain reaction techniques. Central arterial stiffness was measured as carotid‐femoral pulse wave velocity (cfPWV; m/s). Multiple linear regression analyses were used to examine the associations between ACEs, TL, mtDNAcn, and cfPWV. ACEs were positively associated with cfPWV ( β =0.147, P =0.035). TL ( β =−0.170, P =0.011) and mtDNAcn ( β =−0.159, P =0.019) were inversely associated with cfPWV. Neither TL ( β =−0.027, P =0.726) nor mtDNAcn ( β =0.038, P =0.620) was associated with ACEs. Neither marker mediated the association between ACEs and cfPWV.

Conclusions

An increasing number of ACEs were associated with a faster cfPWV and thus, a greater degree of central arterial stiffness. ACEs were not associated with either TL or mtDNAcn, suggesting that these markers do not represent a mediating pathway linking ACEs to central arterial stiffness.

Measurement of yield and quality of DNA in human buffy coat is extraction method dependent

During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.

Use of polypyrrole-polystyrene membranes for extracting DNA from plant tissues

We describe the preparation of a membrane composed of polypyrrole-polystyrene (PPy-PS) and its application in DNA extraction. We adopted the electrospinning technique to prepare polystyrene (PS) membranes, which we used as substrates for incorporating polypyrrole chains through an in situ chemical procedure. As a model system, we initially investigated the use of PPy-PS membranes for the extraction of salmon sperm DNA from aqueous solutions. These studies have shown that the PPy-PS membrane has a maximum adsorption capacity of 236.0 mg of DNA per gram of PPy after 30 min of exposure to a DNA solution (100 mg/L). We incorporated the PPy-PS membranes into centrifugation columns, which we used to carry out experiments for extracting and purification of DNA from curly lettuce leaves. The protocol was initially optimized by first examining the most appropriate concentration of the three components of the lysis buffer (Tris/HCl, NaCl, and EDTA-Na). We then investigated the most adequate volumes of the concentrated surfactant solution (SDS 20%) and that used in the protein and polysaccharide precipitation step (5 M potassium acetate, pH 6.3), factors that directly influence the quality and quantity of the fraction of DNA obtained. For curly lettuce leaves, both in their mature and young stages, the yield and purity of the DNA purified using the PPy-PS membrane were comparable to those obtained using a commercial kit. In both cases, the collected DNA samples presented excellent integrity and quality. These results are suggestive that these composite membranes are competitive with the commercial kits available for the extraction and purification of DNA from plants.

Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study

Background

The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations.

Methods

Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques.

Results

Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions.

Conclusion

Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.

A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits

BACKGROUND

DNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent.

METHODS

We developed a new protocol (IARCp) to improve the quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp's performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit.

RESULTS

Total DNA yield for QG ranged from 120.0 to 282.0 ng (mean 216.5 ng), for MN: 213.6-394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments by spectrophotometer, fluorometer, and real-time PCR assay.

CONCLUSION

Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. This protocol does not require the use of any commercial kits or phenol for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries.

Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities

The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4–13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include Fodinomyces, Penicillium, Recurvomuces, Trichoderma, and Xenoacremonium; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.

Association of a miRNA-binding site polymorphism in IL-16 gene with disease risk and clinical characteristics of rheumatoid arthritis and systemic lupus erythematosus

INTRODUCTION

/objectives. Single nucleotide polymorphisms (SNPs) located at the 3'-UTR region of the target genes of microRNAs (miRNAs) can dysregulate their expression via disrupting the binding site of miRNAs. Interleukin-16 (IL-16) is involved in the pathogenesis of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In the current study, we assessed the possible association between rs1131445 polymorphism in IL-16 gene with risk and clinical characteristics of RA and SLE in the Iranian population.

METHODS

In this case-control study, 120 patients with RA, 120 patients with SLE, and 120 unrelated healthy subjects were collected to estimate rs1131445 (T > C) polymorphism in IL-16 gene using real-time PCR high-resolution melting (HRM) method.

RESULTS

Our results demonstrated considerable associations between TC genotype and C allele of rs1131445 with enhanced risk of RA (OR_{for TC genotype} = 3.01; 95%CI [1.667-5.526], P < 0.001; OR_{for C allele} = 1.96; 95%CI [1.314-2.941], P < 0.001). Besides, there was a marginal association between CC genotype and increased risk of RA (P: 0.031). However, there was an insignificant correlation between genotypes and allele frequencies of rs1131445 with incidence risk of SLE (P > 0.05). Moreover, stratification analysis indicated that the C allele in rs1131445 was linked with disease activity-associated laboratory parameters such as CRP and ESR in both RA and SLE patients, as well as the higher incidence of neurological symptoms in SLE subjects (P < 0.05).

CONCLUSION

These results proposed a significant association between IL-16 polymorphism and augmented risk of RA and clinical characteristics of RA and SLE.

Genetic Analysis of Forty MLPA-Negative Duchenne Muscular Dystrophy Patients by Whole-Exome Sequencing

This manuscript aimed to determine the underlying point mutations causing Duchenne muscular dystrophy (DMD) in a heterogeneous group of Iranian patients, who are clinically suspected. Whole-exome sequencing was utilized to detect disease-causing variants in 40 MLPA-negative DMD patients. Disease-causing variants were detected in the DMD gene in 36/40 of the patients (90%), and 4/40 of them (10%) remained undiagnosed. WES analysis revealed that nonsense variant was the most common type in our study (23/36 of the cases). Besides, 12/36 of the cases had frameshift variant, and one of the patients had a likely pathogenic splice variant in the DMD gene. Carrier testing revealed that 21/40 of the mothers had the identified variant. Therefore, most variants were inherited (58.3%), while 19/40 were de novo (41. 7%). The present study has demonstrated the importance of performing WES to detect disease-causing point mutations in MLPA-negative DMD patients and to identify carrier females. Due to regulatory challenges, the clinical development of therapeutic approaches is time-consuming and may not be available to all patients shortly. Therefore, it appears that the techniques used to accurately detect disease-causing variants in carrier mothers are a more efficient solution to prevent the increased prevalence of DMD.

Recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a threatened species

This study addresses the use of recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a snake species threatened due to over–exploitation and habitat destruction. For its conservation, an efficient species identification method is urgently neededto fight against illegal capture and trade. Fourteen individuals representing 12 snake species (including D. acutus and other snake species) were collected from mountainous regions in Southern China. Genomic DNA was extracted within five minutes by a modified alkaline lysis method. Species–specific primers for recombinase polymerase amplification (RPA) were designed based on the sequences of cytochrome C oxidase subunit I (COI) barcode region, and an optimized RPA assay system was set up. Specificity and sensitivity of the assay were checked, and the assay was validated by identifying 10 commercial Qi She crude drug samples derived from D. acutus. Under optimized RPA conditions, a distinct single band of 354 bp was amplified only for D. acutus but not for the related snake species. The entire procedure can be completed in 30 min at room temperature. Commercial Qi She crude drug identification validated effectiveness of the established assay system. Using a recombinase polymerase amplification (RPA) assay with rapid DNA extraction, we established an on–spot D. acutus identification method with good specificity and sensitivity. This method could become an efficient tool for rigorous supervision of illegal D. acutus capture and trade.

Molecular Identification of Lobster Species Based on Cytochrome Oxidase Subunit I Gene characters

&lt;b&gt;Background and Objective:&lt;/b&gt; In the puerulus phase, which is not pigmented, identification of lobster species based on morphological characteristics is still difficult identity, so it is necessary to identify based on molecular characters. This study aimed to analyze the mitochondrial subunit I cytochrome oxidase (COI) gene characters of the puerulus of lobster species. &lt;b&gt;Materials and Methods:&lt;/b&gt; The data can be useful for developing lobster seed identification methods based on DNA characteristics. Location of lobster sampling in Staring Bay, coastal waters of Moramo District, South Konawe Regency, Indonesia. The molecular characterization method is carried out in several stages, namely specific primer design, DNA preparation, PCR with specific primers, DNA sequencing and DNA sequence analysis. Characteristics of COI gene fragments were analyzed using BLAST analysis, restriction enzyme analysis and phylogenetic tree analysis. &lt;b&gt;Results:&lt;/b&gt; The results showed that DNA was successfully isolated with a high level of purity. The results of the amplification of the COI gene fragment showed thick and firm bands and formed a single band measuring 751 bp with 249 amino acids. Based on the BLAST analysis shows that the COI gene fragment has 99% similarity with &lt;i&gt;Panulirus homarus&lt;/i&gt;. Based restriction enzyme analysis shows that the site of recognition and restriction enzyme cutting position in the &lt;i&gt;Panulirus&lt;/i&gt; COI gene fragment is the same as &lt;i&gt;Panulirus homarus&lt;/i&gt; in Genebank, the &lt;i&gt;Ase&lt;/i&gt;I enzyme in position 392 and &lt;i&gt;Psi &lt;/i&gt;I in positions 47 and 106. &lt;b&gt;Conclusion:&lt;/b&gt; Based on phylogenetic tree analysis, the COI gene fragment is in one group with &lt;i&gt;Panulirus homarus&lt;/i&gt; and has a bootstrap value of 100% which shows that the nucleotide sequence is stable. The three analyzes show that the DNA source organism is the same species as &lt;i&gt;Panulirus homarus&lt;/i&gt;.

Unveiling the K+-sensitivity of cell metabolism using genetically encoded, FRET-based K+, glucose, and ATP biosensors

Investigating dynamic changes of mitochondrial ATP and cytosolic glucose levels of single living cells over time by genetically encoded biosensors provides an informative readout of their metabolic activities. Here, we describe how to monitor the metabolic K⁺-sensitivity of HEK293 cells exploiting ATP-, glucose-, and K⁺ probes. Fluorescence live-cell imaging of these Förster resonance energy transfer-based biosensors over time in response to gramicidin, an ionophoric peptide, indicated an absolute dependency of cellular ATP homeostasis on high intracellular K⁺ levels. For complete information on the generation and use of this protocol please refer to Bischof et al. (2021).

A modified approach for high-quality RNA extraction of spore-forming Bacillus subtilis at varied physiological stages

BACKGROUND

High quality RNA is required for the molecular study. Sample preparation of the spore-forming, Gram-positive bacteria like Bacillus sp., remains challenging although several methods have been proposed. Those techniques were simply developed using cell samples at certain growth stages despite some molecular studies like transcriptomic analyses require RNA samples from different physiological stages.

METHODS AND RESULTS

We developed the rapid, simple yet effective cell-lysis technique with limit use of harsh reagents by modifying the kit-based protocols. Appropriate lysozyme loading (20 mg/mL), incubation time (30 min), and temperature (37 °C) enabled cell lysis and enhanced RNA extraction from both vegetative cells and endospores of Bacillus subtilis TL7-3. High RNA Integrity Numbers and ratios of A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀ of all RNA products collected during the batch cultivation confirmed that invert mixing with absolute ethanol prevented RNA damage during protein denaturation. With the process modification of the major steps in cell lysis and RNA extraction compared with the kit-based protocols that are typically used in laboratory work, interestingly, our modified protocol, simple-yet-effective, yielded higher concentration, purity, and integrity of RNA products from all cell samples collected at different physiological stages. While the kit-based protocols either failed to provide high RNA concentration or RNA purity and integrity for all cell samples particularly during the late-log, stationary, or sporulation.

CONCLUSIONS

Therefore, we can claim the significance of this modified protocol to be applicable for RNA extraction to those spore-forming Gram-positive bacteria not limited to B. subtilis growing at varied physiological stages.

Application of Non-Destructive Methods: Biomarker Assays in Blood of White Stork (Ciconia ciconia) Nestlings

White stork (Ciconia ciconia) nestlings can provide quantitative information on the quality of the surrounding environment by indicating the presence of pollutants, as they depend on locally foraged food. This study represents the first comparison of biomarkers in two fractions of white stork nestling blood: plasma and S9 (the post-mitochondrial fraction). The aim of this study was to evaluate acetylcholinesterase (AChE), carboxylesterase (CES), glutathione S-transferase (GST), and glutathione reductase (GR), as well as to establish a novel fluorescence-based method for glutathione (GSH) and reactive oxygen species (ROS) detection in plasma and S9. Considering the enzymatic biomarkers, lower variability in plasma was detected only for AChE, as CES, GST, and GR had lower variability in S9. Enzyme activity was higher in plasma for AChE, CES, and GST, while GR had higher activity in S9. Regarding the fluorescence-based method, lower variability was detected in plasma for GSH and ROS, although higher GSH detection was reported in S9, and higher ROS was detected in plasma. The present study indicated valuable differences by successfully establishing protocols for biomarker measurement in plasma and S9 based on variability, enzyme activity, and fluorescence. For a better understanding of the environmental effects on nestlings' physiological condition, biomarkers can be measured in plasma and S9.

Biodegradation of used polyethylene bags by a new marine strain of Alcaligenes faecalis LNDR-1

Disposable plastic bags of two different chemical compositions and colors were remediated by the application of novel mesophilic group of bacteria isolated from the banks of sea water, using a 10 week soil burial method. The new strain, LNDR-1, was identified as Alcaligens faecalis by its morphological features and 16S rRNA sequencing. LNDR-1 was able to produce extracellular enzymes such as lipase, CMCase, xylanase, and protease, having PET surface degrading activity. It was found that LNDR-1 had a better decay rate of 15.25 ± 1% and 21.72 ± 2.1% for black and white plastic bags respectively in 10 weeks without prior oxidation as compared to S. marcescens. Polyethylene degradation was confirmed by substantial weight loss, alterations in surface topology, and hydrophobicity index and was found to be directly proportional to the ability to form biofilm on the plastic surface. FTIR results suggest presence of different metabolites in the bags treated with bacterial biofilm in comparison to the control setup inferring various types of metabolic pathways. Present study also reveals the ability of the strain to utilize the used polyethylene bag as the carbon source, without any prior treatment, and as per the literature survey, the working strain is with the capacity to biodegrade plastic at a considerably appreciable rate. This study suggests effectual method for the mechanism of biodegradation of plastic mediated by extracellular enzymes and formation of biofilm.

Development and Evaluation of Solid Witepsol Nanoparticles for Gene Delivery

Objectives

Gene therapy approaches have become increasingly attractive in the medical, pharmaceutical, and biotechnological industries due to their applicability in the treatment of diseases with no effective conventional therapy. Non-viral delivery using cationic solid lipid nanoparticles (cSLNs) can be useful to introduce large nucleic acids to target cells. A careful selection of components and their amounts is critical to obtain a successful delivery system. In this study, solid Witepsol nanoparticles were formulated, characterized, and evaluated in vitro for gene delivery purposes.

Materials and Methods

Solid Witepsol nanoparticles were formulated through the microemulsion dilution technique using two grades of Witepsol and three surfactants, namely Cremephor RH40, Kolliphor HS15, and Peceol. Dimethyldioctadecylammonium bromide was incorporated into the system as a cationic lipid. Twelve combinations of these ingredients were formulated. The obtained nanoparticles were then evaluated for particle size, zeta potential, DNA binding and protection ability, cytotoxicity, and transfection ability.

Results

Particle sizes of the prepared cationic cSLNs were between 13.43±0.06 and 68.80±0.78 nm. Their zeta potential, which is important for DNA binding efficiency, was determined at >+40 mV. Gel retardation assays revealed that the obtained cSLNs can form a compact complex with plasmid DNA (pDNA) encoding green fluorescent protein and that this complex can protect pDNA from DNase I-mediated degradation. Cytotoxicity evaluation of nanoparticles was performed on the L929 cell line. In vitro transfection data revealed that solid Witepsol nanoparticles could effectively transfect fibroblasts.

Conclusion

Our findings indicate that solid Witepsol nanoparticles prepared using the microemulsion dilution technique are promising non-viral delivery systems for gene therapy.

Retrieving high-quality genomic DNA from formalin-fixed paraffin-embedded tissues for multiple molecular analyses

Formalin-fixed paraffin-embedded (FFPE) tissues represent the biggest source of archival materials for molecular biology research and pathology investigations. Nevertheless, fixation by formalin may cause denaturation and modification of macromolecules constraining DNA quality and its downstream applications. In this study, we developed a fast, simple, and cost-effective phenol/chloroform-based protocol for the extraction of high-quality DNA from 101 FFPE colorectal cancer tissue blocks that can be used in multiple molecular studies. DNA samples extracted using this phenol/chloroform protocol and the QIAamp DNA FFPE Tissue kit were evaluated for the quantity, quality, and amplificability. Spectrophotometer analyses revealed significantly higher quality and quantity of DNA samples obtained with the phenol/chloroform protocol as compared to those of the QIAamp DNA FFPE Tissue kit. In addition, the amplificability of these samples as assessed by conventional and multiplex polymerase chain reaction (PCR), followed by sequencing and fragment analyses presented an absolute success rate. Additionally, it is able to amplify a DNA fragment of 725 base-pairs at an adequate amount for downstream applications. This fast, simple, and cost-effective method may facilitate the molecular analyses of a large number of FFPE specimens that best suits the needs of the overall study design in terms of the quality and quantity of the extracted DNA.

Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes

Background

The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time.

Results

11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity.

Conclusions

A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-021-00695-6.

Effects of CYP3A5 Polymorphism on Rapid Progression of Chronic Kidney Disease: A Prospective, Multicentre Study

Personalised medicine is potentially useful to delay the progression of chronic kidney disease (CKD). The aim of this study was to determine the effects of CYP3A5 polymorphism in rapid CKD progression. This multicentre, observational, prospective cohort study was performed among adult CKD patients (≥18 years) with estimated glomerular filtration rate (eGFR) ≥30 mL/min/1.73 m2, who had ≥4 outpatient, non-emergency eGFR values during the three-year study period. The blood samples collected were analysed for CYP3A5*3 polymorphism. Rapid CKD progression was defined as eGFR decline of >5 mL/min/1.73 m2/year. Multiple logistic regression was then performed to identify the factors associated with rapid CKD progression. A total of 124 subjects consented to participate. The distribution of the genotypes adhered to the Hardy-Weinberg equilibrium (X2 = 0.237, p = 0.626). After adjusting for potential confounding factors via multiple logistic regression, the factors associated with rapid CKD progression were CYP3A5*3/*3 polymorphism (adjusted Odds Ratio [aOR] 4.190, 95% confidence interval [CI]: 1.268, 13.852), adjustments to antihypertensives, young age, dyslipidaemia, smoking and use of traditional/complementary medicine. CKD patients should be monitored closely for possible factors associated with rapid CKD progression to optimise clinical outcomes. The CYP3A5*3/*3 genotype could potentially be screened among CKD patients to offer more individualised management among these patients.

How the 'kitome' influences the characterization of bacterial communities in lepidopteran samples with low bacterial biomass

AIMS

We aimed to elucidate whether the DNA extraction kit and bacteria therein affect the characterization of bacterial communities associated with butterfly samples harbouring different bacterial abundancies.

METHODS AND RESULTS

We analysed bacteria associated with eggs of Pieris brassicae and with adults of this butterfly, which were either untreated or treated with antibiotics (ABs). Three DNA extraction kits were used. Regardless of the extraction kit used, PCR amplification of the bacterial 16S rRNA gene detected very low bacterial presence in eggs and AB-treated butterflies. In untreated butterflies, bacterial signal intensity varied according to the kit and primers used. Sequencing (MiSeq) of the bacterial communities in untreated and AB-treated butterflies revealed a low alpha diversity in untreated butterflies because of the dominance of few bacteria genera, which were detectable regardless of the kit. However, a significantly greater alpha diversity was found in AB-treated butterflies, evidencing a true bias of the results due to bacterial contaminants in the kit.

CONCLUSIONS

The so-called 'kitome' can impact the profiling of Lepidoptera-associated bacteria in samples with low bacterial biomass.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study highlights the necessity of method testing and analysis of negative controls when investigating Lepidoptera-associated bacterial communities.

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

Metagenomic applications in exploration and development of novel enzymes from nature: a review

BACKGROUND

Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research.

SHORT CONCLUSION

Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.

Robust DNA protocols for tropical soils

Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.

Reliable approaches to extract high-integrity RNA from skin and other pertinent tissues used in pain research

Introduction

Comprehensive mRNA sequencing is a powerful tool for conducting unbiased, quantitative differential gene expression analysis. However, the reliability of these data is contingent on the extraction of high-quality RNA from samples. Preserving RNA integrity during extraction can be problematic, especially in tissues such as skin with dense, connective matrices and elevated ribonuclease expression. This is a major barrier to understanding the influences of altered gene expression in many preclinical pain models and clinical pain disorders where skin is the site of tissue injury.

Objective

This study developed and evaluated extraction protocols for skin and other tissues to maximize recovery of high-integrity RNA needed for quantitative mRNA sequencing.

Methods

Rodent and human tissue samples underwent one of the several different protocols that combined either RNA-stabilizing solution or snap-freezing with bead milling or cryosectioning. Indices of RNA integrity and purity were assessed for all samples.

Results

Extraction of high-integrity RNA is highly dependent on the methods used. Bead-milling skin collected in RNA-stabilizing solution resulted in extensive RNA degradation. Snap-freezing in liquid nitrogen was required for skin and highly preferable for other tissues. Skin also required cryosectioning to achieve effective penetration of RNA-stabilizing solution to preserve RNA integrity, whereas bead milling could be used instead with other tissues. Each method was reproducible across multiple experimenters. Electrophoretic anomalies that skewed RNA integrity value assignment required manual correction and often resulted in score reduction.

Conclusion

To achieve the potential of quantitative differential gene expression analysis requires verification of tissue-dependent extraction methods that yield high-integrity RNA.

Membrane-sensitive bacterial DNA extractions and absolute quantitation of recovery efficiencies

Absolute quantification of waterborne pathogens is mandatory for microbiological risk assessment (MRA). Determination of the DNA recovery efficiency is an essential step before the quantitative molecular measurements, which has been largely ignored. In this study, we compared the DNA recovery efficiency and quality of five extraction methods, including two modified phenol-chloroform-based extractions with mechanical shearing and three commercial kits for the extraction of DNA from indigenous mixed-bacteria culture of river water. All of the methods gave relatively satisfying results from the pelleted sample through centrifugation. However, the commercial kits provided surprisingly low DNA yields for membrane-filtered samples because of DNA trapping and/or absorption on the membrane. Integrating with enzymatic lysis, bath sonication, phenol extraction, and alcohol precipitation achieved highest DNA yields and an acceptable DNA integrity for quantitative PCR. A plasmid containing the human GADPH gene fragment was demonstrated to be a suitable spiking control for determining the absolute DNA recovery efficiency. The unexpectedly low efficiencies of commercial kit extractions imply the significant underestimation of pathogenic bacteria in previous studies, which should gain enough concern in the area of pathogen monitoring in the future.

Moving tissue spectral window to the deep-ultraviolet via optical clearing

The optical immersion clearing technique has been successfully applied through the last 30 years in the visible to near infrared spectral range, and has proven to be a promising method to promote the application of optical technologies in clinical practice. To investigate its potential in the ultraviolet range, collimated transmittance spectra from 200 to 1000 nm were measured from colorectal muscle samples under treatment with glycerol-water solutions. The treatments created two new optical windows with transmittance efficiency peaks at 230 and 300 nm, with magnitude increasing with glycerol concentration in the treating solution. Such discovery opens the opportunity to develop clinical procedures to perform diagnosis or treatments in the ultraviolet.

A novel method to optimise the utility of underused moulted plumulaceous feather samples for genetic analysis in bird conservation

Non-invasive sampling methods are increasingly being used in conservation research as they reduce or eliminate the stress and disturbance resulting from invasive sampling of blood or tissue. Here we present a protocol optimised for obtaining usable genetic material from moulted plumulaceous feather samples. The combination of simple alterations to a ‘user-developed’ method, comprised of increased incubation time and modification of temperature and volume of DNA elution buffer, are outlined to increase DNA yield and significantly increase DNA concentration (W = 81, p < 0.01, Cohens’s d = 0.89). We also demonstrate that the use of a primerless polymerase chain reaction (PCR) technique increases DNA quality and amplification success when used prior to PCR reactions targeting avian mitochondrial DNA (mtDNA). A small amplicon strategy proved effective for mtDNA amplification using PCR, targeting three overlapping 314–359 bp regions of the cytochrome oxidase I barcoding region which, when combined, aligned with target-species reference sequences. We provide evidence that samples collected non-invasively in the field and kept in non-optimal conditions for DNA extraction can be used effectively to sequence a 650 bp region of mtDNA for genetic analysis.

Metagenomics analysis of bacterial structure communities within natural biofilm

The bacterial profiles of natural household biofilm have not been widely investigated. The majorities of these bacterial lineages are not cultivable. Thus, this study aims (i) to enumerate some potential bacterial lineages using culture based method within biofilm samples and confirmed using Biolog GEN III and polymerase chain reaction (PCR). (ii) To investigate the bacterial profiles of communities in two biofilm samples using next generation sequencing (NGS). Forty biofilm samples were cultured and colonies of each selected prevailing potential lineages (E. coli, Salmonella entrica, Pseudomonas aeruginosa, Staphylococcus aureus and Listeria monocytogenes) were selected for confirmation. From obtained results, the counts of the tested bacterial lineages in kitchen biofilm samples were greater than those in bathroom samples. Precision of PCR was higher than Biolog GEN III to confirm the bacterial isolates. Using NGS analysis, the results revealed that a total of 110,554 operational taxonomic units (OTUs) were obtained for two biofilm samples, representing kitchen and bathroom biofilm samples. The numbers of phyla in the kitchen biofilm sample (35 OTUs) was higher than that in bathroom sample (18 OTUs). A total of 435 genera were observed in the bathroom biofilm sample compared to only 256 in the kitchen sample. Evidences have shown that the empirical gadgets for biofilm investigation are becoming convenient and affordable. Many distinct bacterial lineages observed in biofilm are one of the most significant issues that threaten human health and lead to disease outbreaks.

On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option?

Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.

Synthesis, Characterization, and Application of Poly(4,4'-Cyclohexylidene Bisphenol Oxalate) for Solid-Phase Extraction of DNA

The present study has synthesized poly(4,4'-cyclohexylidene bisphenol oxalate) by the condensation of oxalyl chloride with 4,4'-cyclohexylidene bisphenol, where its efficacy was tested for the solid-phase extraction of DNA. The synthesized polymer in the form of a white powder was characterized by FTIR, TGA-DTG, SEM, and BET analysis. The study utilized solid-phase application of the resulting polymer to extract DNA. The analysis of results provided the information that the extraction efficiency is a strong dependent of polymer amount and binding buffer type. Among the three types of buffers tested, the GuHCl buffer produced the most satisfactory results in terms of yield and efficiency of extraction. Moreover, the absorbance ratio of A260/A280 in all of the samples varied from 1.682 to 1.491, thereby confirming the capability of poly(4,4'-cyclohexylidene bisphenol oxalate) to elute pure DNA. The results demonstrated an increased DNA binding capacity with respect to increased percentage of the polymer. The study has concluded that poly(bisphenol Z oxalate) can be applied as one of the potential candidates for the high efficiency extraction of DNA by means of a simple, cost-effective, and environmentally friendly approach compared to the other traditional solid-phase methods.

A Nucleic Acid Quality Control Strategy for Frozen Tissues from a Biobank of High-Risk Pregnancy

BACKGROUND

The preservation of placental and fetal tissues will contribute to studying the pathogenesis of high-risk pregnancy diseases. However, few studies have focused on the effects of different preservation methods and cold ischemia time (CIT) on the quality of nucleic acids. An available quality control (QC) strategy will be beneficial to evaluate these effects for high-risk pregnancy biobanks.

METHODS

We established an evaluation strategy of nucleic acid QC by analyzing total RNA and genomic DNA (gDNA). Through this strategy, the effects of CIT, cryoprotectants (CPAs), and freeze/thaw cycles on the yield and integrity of placental RNA were analyzed. In addition, the effects of CIT on the yield and integrity of fetal DNA were determined.

RESULTS

For placental samples, there was no significant difference in RNA integrity (CIT <2 hours). After several freeze/thaw cycles, the RNA quality number values of placental samples in the CPA-free group and in the RNasin (TRIzol) group were decreased. For fetal samples, the DNA integrity of different organs (CIT <24 hours) was completely satisfactory, but it declined with the extension of CIT. Furthermore, different organs had different tolerances to cold ischemia, and the rank was as follows: skin, heart, liver, and placenta. In addition, the content of medium-length (600 bp) and long (1310 bp) fragments of gDNA were mainly reduced with the extension of CIT.

CONCLUSION

The RNA integrity of placental tissue was affected by CIT significantly. It is recommended that placenta should be cryopreserved within 2 hours (4°C) from isolation. To ensure DNA quality of fetal tissues, the samples are suggested to be frozen within 24 hours (4°C) from isolation. On the contrary, if samples have a long CIT, skin is superior to other organs in the aspect of biobanking donor's genetic information.

Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue

The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules. We conducted a systematic examination of nucleic acids and proteins co-extracted from 118 FFPE blocks sampled from the AIDS and Cancer Specimen Resource (ACSR) at The George Washington University after stratification by storage duration and the three most common tumor tissue types at the ACSR (adenocarcinoma, squamous cell carcinoma, and papillary carcinoma). DNA, RNA, miRNA, and protein could be co-extracted from 98% of the FFPE blocks sampled, with DNA and miRNA "fit" for diverse genomic purposes including sequencing. While RNA was the most labile of the FFPE derivatives, especially when assessed by RNA integrity number (RIN), it was still "fit" for genomic methods that use smaller sequence lengths, e.g., quantitative PCR. While more than half of the protein derivatives were fit for proteomic purposes, our analyses indicated a significant interaction effect on the absorbance values for proteins derived from FFPE, implying that storage duration may affect protein derivatives differently by tumor tissue type. The mean absorbance value for proteins derived from more recently stored FFPE was greater than protein derived from older FFPE, with the exception of adenocarcinoma tissue. Finally, the fitness of one type of derivative was weakly associated with the fitness of derivatives co-extracted from the same FFPE block. The current study used several novel quality assurance approaches and metrics to show that archival FFPE tissue blocks are a valuable resource for contemporary genomic and proteomic platforms.

Superresolution Imaging of Clinical Formalin Fixed Paraffin Embedded Breast Cancer with Single Molecule Localization Microscopy

Millions of archived formalin-fixed, paraffin-embedded (FFPE) specimens contain valuable molecular insight into healthy and diseased states persevered in their native ultrastructure. To diagnose and treat diseases in tissue on the nanoscopic scale, pathology traditionally employs electron microscopy (EM), but this platform has significant limitations including cost and painstaking sample preparation. The invention of single molecule localization microscopy (SMLM) optically overcame the diffraction limit of light to resolve fluorescently labeled molecules on the nanoscale, leading to many exciting biological discoveries. However, applications of SMLM in preserved tissues has been limited. Through adaptation of the immunofluorescence workflow on FFPE sections milled at histological thickness, cellular architecture can now be visualized on the nanoscale using SMLM including individual mitochondria, undulations in the nuclear lamina, and the HER2 receptor on membrane protrusions in human breast cancer specimens. Using astigmatism imaging, these structures can also be resolved in three dimensions to a depth of ~800 nm. These results demonstrate the utility of SMLM in efficiently uncovering ultrastructural information of archived clinical samples, which may offer molecular insights into the physiopathology of tissues to assist in disease diagnosis and treatment using conventional sample preparation methods.