Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy

The landscape of hepatitis B virus(HBV)integration in the plasma cell-free DNA(cfDNA)of HBV-infected patients with different stages of liver diseases[chronic hepatitis B(CHB),liver cirrhosis(LC),and hepatocellular carcinoma(HCC)]remains unclear.In this study,we developed an improved strategy for detecting HBV DNA integration in plasma cfDNA,based on DNA probe capture and next-generation sequencing.Using this optimized strategy,we successfully detected HBV integration events in chimeric artificial DNA samples and HBV-infected HepG2-NTCP cells at day one post infection,with high sensitivity and accuracy.The characteristics of HBV integration events in the HBV-infected HepG2-NTCP cells and plasma cfDNA from HBV-infected individuals(CHB,LC,and HCC)were further investigated.A total of 112 and 333 integration breakpoints were detected in the HepG2-NTCP cells and 22 out of 25(88%)clinical HBV-infected samples,respectively.In vivo analysis showed that the normalized number of support unique sequences(nnsus)in HCC was significantly higher than in CHB or LC patients(P values<0.05).All integration breakpoints are randomly distributed on human chromosomes and are enriched in the HBV genome around nt 1800.The majority of integration breakpoints(61.86%)are located in the gene-coding region.Both non-homologous end-joining(NHEJ)and microhomology-mediated end-joining(MMEJ)interactions occurred during HBV integration across the three different stages of liver diseases.Our study provides evidence that HBV DNA integration can be detected in the plasma cfDNA of HBV-infected patients,including those with CHB,LC,or HCC,using this optimized strategy.

Chromatin condensation but not DNA integrity of pig sperm is greater in the sperm-rich fraction

Background Protamination and condensation of sperm chromatin as well as DNA integrity play an essential role during fertilization and embryo development.In some mammals,like pigs,ejaculates are emitted in three separate fractions:pre-sperm,sperm-rich(SRF)and post sperm-rich(PSRF).These fractions are known to vary in volume,sperm concentration and quality,as well as in the origin and composition of seminal plasma(SP),with differences being also observed within the SRF one.Yet,whether disparities in the DNA integrity and chromatin condensation and pro-tamination of their sperm exist has not been interrogated.Results This study determined chromatin protamination(Chromomycin A3 test,CMA_(3)),condensation(Dibromobi-mane test,DBB),and DNA integrity(Comet assay)in the pig sperm contained in the first 10 m L of the SRF(SRF-P1),the remaining portion of the sperm-rich fraction(SRF-P2),and the post sperm-rich fraction(PSRF).While chromatin protamination was found to be similar between the different ejaculate fractions(P>0.05),chromatin condensation was seen to be greater in SRF-P1 and SRF-P2 than in the PSRF(P=0.018 and P=0.004,respectively).Regarding DNA integrity,no differences between fractions were observed(P>0.05).As the SRF-P1 has the highest sperm concentra-tion and ejaculate fractions are known to differ in antioxidant composition,the oxidative stress index(OSi)in SP,calcu-lated as total oxidant activity divided by total antioxidant capacity,was tested and confirmed to be higher in the SRF-P1 than in SRF-P2 and PSRF(0.42±0.06 vs.0.23±0.09 and 0.08±0.00,respectively;P<0.01);this index,in addition,was observed to be correlated to the sperm concentration of each fraction(Rs=0.973;P<0.001).Conclusion While sperm DNA integrity was not found to differ between ejaculate fractions,SRF-P1 and SRF-P2 were observed to exhibit greater chromatin condensation than the PSRF.This could be related to the OSi of each fraction.

The Calculation of Parameters for DNA Kinetic Structure Based on Monte-Carlo Multiple Integrals

Based on protein-DNA complex crystal structural data in up-to-date Nucleic Acid Database,the related parameters of DNA Kinetic Structure were investigated by Monte-Carlo Multiple Integrals on the base of modified DNA structure statistical mechanical model,and time complexity and precision were analyzed on the calculated results.

Effect of Cadmium on Rat Leydig Cell Testosterone Production and DNA Integrity in vitro

Cadmium （Cd） is an elemental heavy metal with widely recognized toxicity. Its long-term use in industrial processes and daily activities has caused alarming levels of Cd contamination in the natural environment. According to the estimates by the Agency of Toxic Substances and Disease Registry in the US, 25 000 to 30 000 metric tons of Cd is annually released to the environment . Results of previous studies have demonstrated that several organs are targets of Cd, but the most important of these targeted organs may be the testes.

Development of a droplet digital polymerase chain reaction assay for the sensitive detection of total and integrated HIV-1 DNA

Background:Total human immunodeficiency virus(HIV)DNA and integrated HIV DNA are widely used markers of HIV persistence.Droplet digital polymerase chain reaction(ddPCR)can be used for absolute quantification without needing a standard curve.Here,we developed duplex ddPCR assays to detect and quantify total HIV DNA and integrated HIV DNA.Methods:The limit of detection,dynamic ranges,sensitivity,and reproducibility were evaluated by plasmid constructs containing both the HIV long terminal repeat(LTR)and human CD3 gene(for total HIV DNA)and ACH-2 cells(for integrated HIV DNA).Forty-two cases on stable suppressive antiretroviral therapy(ART)were assayed in total HIV DNA and integrated HIV DNA.Correlation coefficient analysis was performed on the data related to DNA copies and cluster of differentiation 4 positive(CD4^(+))T-cell counts,CD8^(+)T-cell counts and CD4/CD8 T-cell ratio,respectively.The assay linear dynamic range and lower limit of detection(LLOD)were also assessed.Results:The assay could detect the presence of HIV-1 copies 100%at concentrations of 6.3 copies/reaction,and the estimated LLOD of the ddPCR assay was 4.4 HIV DNA copies/reaction(95%confidence intervals[CI]:3.6-6.5 copies/reaction)with linearity over a 5-log_(10)-unit range in total HIV DNA assay.For the integrated HIV DNA assay,the LLOD was 8.0 copies/reaction(95%CI:5.8-16.6 copies/reaction)with linearity over a 3-log 10-unit range.Total HIV DNA in CD4^(+)T cells was positively associated with integrated HIV DNA(r=0.76,P<0.0001).Meanwhile,both total HIV DNA and integrated HIV DNA in CD4^(+)T cells were inversely correlated with the ratio of CD4/CD8 but positively correlated with the CD8^(+)T-cell counts.Conclusions:This ddPCR assay can quantify total HIV DNA and integrated HIV DNA efficiently with robustness and sensitivity.It can be readily adapted for measuring HIV DNA with non-B clades,and it could be beneficial for testing in clinical trials.

Retroviral integrase protein and intasome nucleoprotein complex structures

Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase(IN) protein. IN catalyzes two distinct chemical reactions: 3'-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3'-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980 s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus(PFV). Since then, two additional retroviral intasome structures, from the α-retrovirus Rous sarcoma virus(RSV) and β-retrovirus mouse mammary tumor virus(MMTV), have emerged. Here, we briefly review the history of IN structural biology prior to the intasome era, and then compare the intasome structures of PFV, MMTV and RSV in detail. Whereas the PFV intasome is characterized by a tetrameric assembly of IN around the viral DNA ends, the newer structures harbor octameric IN assemblies. Although the higher order architectures of MMTV and RSV intasomes differ from that of the PFV intasome, they possess remarkably similar intasomal core structures. Thus, retroviral integration machineries have adapted evolutionarily to utilize disparate IN elements to construct convergent intasome core structures for catalytic function.

Sperm cryodamage occurs after rapid freezing phase:flow cytometry approach and antioxidant enzymes activity at different stages of cryopreservation

Background： In order to improve the efficiency of bovine sperm cryopreservation process, it is important to understand how spermatozoa respond to differences in temperature as well as the ability to recover its own metabolism. The combination between flow cytometry approach and antioxidant enzymes activity allows a more sensible evaluation of sperm cell during cryopreservation. The aim of this study was to evaluate sperm attributes and antioxidant enzymes activity during different stages of cryopreservation process. Semen samples from Holstein bulls （n = 4） were separated in 3 treatments： fresh （37 ℃）; cooled （5 ℃）; and thawed. Evaluation occurred at 0 h and 2 h after incubation. Membrane integrity, mitochondrial membrane potential （MMP） and DNA damages were evaluated by flow cytometry; activities of antioxidant enzymes such as catalase, superoxide dismutase and gluthatione peroxidase were measured by spectrofotometry. Results： There was an increase in the percentage of sperm with DNA damage in the thawed group, compared to fresh and cooled, and for 2 hs of incubation when compared to 0 h. Considering MMP, there was an increase in the percentage of cells with medium potential in thawed group when compared to fresh and cooled groups. Opposingly, a decrease was observed in the thawed group considering high mitochondrial potential. Also in the thawed group, there was an increase on cells with damaged acrosome and membrane when compared to fresh and cooled groups. Significant correlations were found between antioxidant enzymes activity and membrane or mitochondrial parameters. Conclusion： Based on our results, we conclude that cryopreservation affects cellular and DNA integrity and that the critical moment is when sperm cells are exposed to freezing temperature. Also, our study indicates that intracellular antioxidant machinery （SOD and GPX enzymes） is not enough to control cryodamage.

Circulating and stool nucleic acid analysis for colorectal cancer diagnosis

In recent years, the need to identify molecular markers characterized by high sensitivity and specificity in detecting and monitoring early and colorectal cancer lesions has increased. Up to now, none of the markers or panels of markers analyzed have met the rigorous standards required of a screening program. The important discovery of circulating nucleic acids in biological fluids has aroused intense scientific interest because of their usefulness in malignant and non malignant diseases. Over time, their yield and stability have been identified and compared with other &#x0201c;standard&#x0201d; biomarkers. The analysis of circulating DNA from blood and stool is a relatively simple and non-invasive procedure, representing a very attractive marker to detect genetic and epigenetic mutations and to monitor disease progression. A correlation between blood and stool biomarkers could also help to enhance currently available diagnostic approaches. However, various processing and analytic problems need to be resolved before such an approach can be applied in clinical practice.

Acetyl-L-carnitine:An Effective Antioxidant against Cryo-damage on Human Spermatozoa with Asthenospermia

A variety of natural and artificial cryoprotectant extenders have been explored to enhance sperm recovery following cryopreservation-thawing process. The current investigation is aimed at evaluating the effect of acetyl-L-carnitine on human spermatozoa and reactive species oxygen（ROS） level after freezing-thawing process. The spermatozoa were collected from 35 male patients diagnosed as having asthenospermia. The cryopreservation of human spermatozoa treated with acetyl-L-carnitine at different concentrations（group B： 2.5 mmol/L, group C： 7.5 mmol/L, group D： 15 mmol/L） was compared with control（group A： no acetyl-L-carnitine given）. For the frozen-thawed spermatozoa, the viability, motility and DNA integrity were measured by comet assay, acrosome integrity by FITC-PNA staining and ROS level was determined in each group. The results showed that there were no significant differences in motility and viability between group A and group B, while the motility and viability of spermatozoa in group C and group D were significantly increased as compared with those in group A. As compared with group A, the values for DNA integrity parameters including comet rate（CR）, tail DNA percentage（TD）, tail length（TL） and Oliver tail moment（OTM） were significantly reduced in group C and group D. Group C and group D also displayed a higher proportion of intact acrosome than group A. No significant difference in ROS level was found between group A and group B, while with the increase in acetyl-L-carnitine concentration, the ROS level in groups C and D was significantly reduced as compared with that in group A. In conclusion, acetyl-L-carnitine at a concentration of 7.5 mmol/L is an effective antioxidant against cryo-damage on post-thawed human spermatozoa.

Implementation of Automated Sample Quality Control in Whole Exome Sequencing

Aims： High-quality DNA as input material for a NGS （next-generation sequencing） workflow is essential for the successful preparation of a DNA library. Additionally, DNA quality has a strong impact on sequencing results. Therefore, it is important to include QC （quality control） steps to assess size, concentration, molarity, and integrity of the DNA during the workflow. Material and Methods： The WES （Whole Exome Sequencing） workflow at the Genomics and Proteomics Core Facility of DKFZ （the German Cancer Research Center） was performed with several QC steps： QC of the input material, QC of intermediate products during library preparation, and QC of final libraries. The Agilent 4200 TapeStation system, which offers automated sample processing, was used to evaluate quantity, size, molarity, and integrity of the samples. Key Findings： The Agilent Genomic DNA ScreenTape assay offers an unbiased genomic DNA integrity assessment, which enables protocol adaption for optimized library preparation, for example, selection of a suitable shearing protocol. Additionally, QC steps during library preparation such as evaluation of library size, concentration, and molarity ensure maximal sequencing output. Significance： The automated and fast high-throughput analysis of genomic DNA with the 4200 TapeStation system helps to save labor time and costs. Additionally, the easy-to-use system can be integrated as a QC tool into the NGS workflow to ensure successful library preparation. QC steps enable the confirmation of suitable library size and concentration for the workflow.

Magnetic-activated cell sorting of nonapoptotic spermatozoa with a high DNA fragmentation index improves the live birth rate and decreases transfer cycles of IVF/ICSI

The present study aimed to evaluate the clinical outcomes of magnetic-activated cell sorting(MACS)in sperm preparation for male subjects with a sperm DNA fragmentation index(DFI)≥30%.A total of 86 patients who had undergone their first long-term long protocol were selected.The protocol involved in vitro fertilization(IVF)and intracytoplasmic sperm injection(ICSI)cycles,and the patients were divided into the MACS or control groups.The MACS group included sperm samples analyzed with MACS that were combined with density gradient centrifugation(DGC)and the swim-up(SU)technique(n=39),and the control group included sperm samples prepared using standard techniques(DGC and SU;n=41).No differences were noted with regard to basic clinical characteristics,number of oocytes retrieved,normal fertilization rate,cleavage rate,or transplantable embryo rate between the two groups in IVF/ICSI.In addition,the clinical pregnancy and implantation rates of the first embryo transfer cycles indicated no significant differences between the two groups.However,there was a tendency to improve the live birth rate(LBR)of the first embryo transfer cycle(63.2%vs 53.9%)and the cumulative LBR(79.5%vs 70.7%)in the MACS group compared with the control group.Moreover,the number of transferred embryos(mean±standard deviation[s.d.]:1.7±0.7 vs 2.3±1.6)and the transfer number of each retrieved cycle(mean±s.d.:1.2±0.5 vs 1.6±0.8)were significantly lower in the MACS group than those in the control group.Thus,the selection of nonapoptotic spermatozoa by MACS for higher sperm DFI could improve assisted reproductive clinical outcomes.

Effects of Rosmarinic Acid on DNA Integrity and H19 Differentially Methylated Region Methylation Levels in Human Sperm Preserved by Freeze-Drying

Original Article Effects of Rosmarinic Acid on DNA Integrity and H19 Differentially Methylated Region Methylation Levels in Human Sperm Preserved by Freeze-Drying Wang Yi-Yu,Zhu Wei-Jie Published 2021-03-25 Cite as Reprod Dev Med,2021,05 Reprod Dev Med,2021,05(1):9-14.DOI:10.4103/2096-2924.309790 Abstract Objective:To investigate the effects of rosmarinic acid(RA)on the DNA integrity and methylation levels of the H19 differentially methylated region(DMR)of freeze-dried human sperm after 1 week and 6 months of storage at 4℃.Methods:Semen samples from 15 healthy normospermic donors were used in this study.The samples were divided into five groups,including the control group with fresh sperm and four experimental groups with freeze-dried sperm(1-week storage with EGTA buffer solution,Group A;1-week storage with EGTA buffer solution containing 105μmol/L RA,Group B;6-month storage with EGTA buffer solution,Group C;and 6-month storage with EGTA buffer solution containing 105μmol/L RA,Group D).DNA integrity was evaluated using the sperm chromatin dispersion test.H19 DMR methylation levels were detected by bisulfite sequencing polymerase chain reaction.Results:After 1 week of storage,no differences in sperm DNA integrity were observed among Groups A,B,and controls(P>0.05).After 6 months of storage,the sperm DNA integrity of Group D did not change significantly compared with that of the control group(P>0.05),whereas that of Group C decreased significantly(P<0.05).There were no differences in H19 DMR methylation levels among the five groups(P>0.05).Conclusions:The DNA integrity of freeze-dried human sperm can be effectively protected by adding RA within 6 months,and the H19 DMR methylation level of human sperm can be maintained for 6 months after freeze-drying.

Recombinase-mediated Gene Stacking as a Transformation Operating System

The current method for combining transgenes into a genome is through the assortment of independent loci, a classical operating system compatible with transgenic traits created by different developers, at different times and/or through different transformation techniques. However, as the number of transgenic loci increases over time, increasingly larger populations are needed to find the rare individual with the desired assortment of transgenic loci along with the non-transgenic elite traits. Introducing a transgene directly into a field cultivar would bypass the need to introgress the engineered trait. However, this necessitates separate transformations into numerous field cultivars, along with the characterization and regulatory approval of each independent transformation event. Reducing the number of segregating transgenic loci could be achieved if multiple traits are introduced at the same time, a preferred option if each of the many traits is new or requires re-engineering. If reengineering of previously introduced traits is not needed, then appending a new trait to an existing locus would be a rational strategy. The insertion of new DNA at a known locus can be accomplished by site- specific integration, through a host-dependent homology-based process, or a heterologous site-specific recombination system. Here, we discuss gene stacking through the use of site-specific recombinases.

Effects of the crude extract of Polygala tenuifolia Willd on human sperm in vitro

The aim of the present study is to analyze sperm membrane changes and the spermicidal effect in treatment with the crude extract from Polygala tenuifo/ia Willd （PTW） in vitro. The root of PTW was extracted in distilled water. Normal human spermatozoa were used to assess the spermicidal activity （Sander-Cramer assay） of the extract from the PTW root. The hypo-osmotic swelling （HOS） test and the eosin Y （EY） staining were used to detect the integrity of sperm membrane and vitality. The sperm chromatin dispersion （SCD） test was performed to determine sperm DNA integrity. N-9 was used as a reference standard and semen added to physiological saline was used as the control. Semen samples were donated by 42 healthy fertile men. The crude extract from the root of PTW could immobilize and kill 100% spermatozoa within 20 s in vitro at the concentrations of 20.0 and 10.0 mg/ml; at the concentration of 5.0 mg/ml, spermatozoa were immobilized in （39.5±3.2） s. In the groups of the crude extract from the root of PTW and N-9 solution the rate of the normal HOS （tails swollen） and the white head （unstained） was 0%, and the rate of the abnormal HOS （tails unswollen） and red head （stained） was 100%. Sperm DNA fragmentation showed no change in exposure to the crude extract from the root of PTW and N-9 solution. The sperm revival test did not show any spermatozoa that recovered their motilities. The rapid spermicidal activity of the crude extract from the root of PTW in vitro may occur by the disruption of the sperm membrane integrity.

Continuous desulfurization and bacterial community structure of an integrated bioreactor developed to treat SO_2 from a gas stream

Sulfide dioxide（SO2） is often released during the combustion processes of fossil fuels. An integrated bioreactor with two sections, namely, a suspended zone（SZ） and immobilized zone（IZ）, was applied to treat SO2 for 6 months. Sampling ports were set in both sections to investigate the performance and microbial characteristics of the integrated bioreactor. SO2 was effectively removed by the synergistic effect of the SZ and IZ, and more than 85%removal efficiency was achieved at steady state. The average elimination capacity of SO2 in the bioreactor was 2.80 g/（m3·hr） for the SZ and 1.50 g/（m3· hr） for the IZ. Most SO2 was eliminated in the SZ. The liquid level of the SZ and the water content ratio of the packing material in the IZ affected SO2 removal efficiency. The SZ served a key function not only in SO2 elimination, but also in moisture maintenance for the IZ. The desired water content in IZ could be feasibly maintained without any additional pre-humidification facilities. Clone libraries of 16 S r DNA directly amplified from the DNA of each sample were constructed and sequenced to analyze the community composition and diversity in the individual zones.The desulfurization bacteria dominated both zones. Paenibacillus sp. was present in both zones, whereas Ralstonia sp. existed only in the SZ. The transfer of SO2 to the SZ involved dissolution in the nutrient solution and biodegradation by the sulfur-oxidizing bacteria.This work presents a potential biological treatment method for waste gases containing hydrophilic compounds.