Comparative of Forensic DNA Identification Using Cell Lysis Method and Magnetic Beads Method / 法医学杂志

OBJECTIVES@#To compare the effects of cell lysis method and magnetic beads method in forensic DNA identification and to explore these two methods in forensic DNA identification.@*METHODS@#The genome DNA of THP-1 cells in different quantities was extracted by the cell lysis method and magnetic beads method, and the DNA content was quantified by real-time quantitative PCR. The cell lysis method and magnetic beads method were used to type the STR of human blood with different dilution ratios.@*RESULTS@#When the numbers of THP-1 cell were 100, 400 and 800, the DNA content extracted by cell lysis method were (1.219±0.334), (5.081±0.335), (9.332±0.318) ng, respectively; and the DNA content extracted by magnetic beads method were (1.020±0.281), (3.634±0.482), (7.896±0.759) ng, respectively. When the numbers of THP-1 cells were 400 and 800, the DNA content extracted by the cell lysis method was higher than that by the magnetic beads method. The sensitivity of cell lysis method and magnetic beads method was similar in STR typing of human blood at different dilution ratios. Complete STR typing could be obtained at 100, 300 and 500-fold dilutions of blood samples, but could not be detected at 700-fold dilution. STR typing of undiluted human blood could not be detected by cell lysis method.@*CONCLUSIONS@#The cell lysis method is easy to operate and can retain template DNA to the maximum extend. It is expected to be suitable for trace blood evidence tests.

In vivo assay to identify bacteria with ß-glucosidase activity

Background: ß-Glucosidase assay is performed with purified or semipurified enzymes extracted from cell lysis. However, in screening studies, to find bacteria with ß-glucosidase activity among many tested bacteria, a fast method without cell lysis is desirable. In that objective, we report an in vivo ß-glucosidase assay as a fast method to find a ß-glucosidase producer strain. Results: The method consists in growing the strains for testing in a medium supplemented with the artificial substrate p-nitrophenyl-ß-glucopyranoside (pNPG). The presence of ß-glucosidases converts the substrate to p-nitrophenol (pNP), a molecule that can be easily measured in the supernatant spectrophotometrically at 405 nm. The assay was evaluated using two Bifidobacterium strains: Bifidobacterium longum B7254 strain that lacks ß-glucosidase activity and Bifidobacterium pseudocatenulatum B7003 strain that shows ß-glucosidase activity. The addition of sodium carbonate during pNP measurement increases the sensitivity of pNP detection and avoids the masking of absorbance by the culture medium. Furthermore, we show that pNP is a stable enzymatic product, not metabolized by bacteria, but with an inhibitory effect on cell growth. The ß-glucosidase activity was measured as units of enzyme per gram per minute per dry cell weight. This method also allowed the identification of Lactobacillus strains with higher ß-glucosidase activity among several lactobacillus species. Conclusion: This in vivo ß-glucosidase assay can be used as an enzymatic test on living cells without cell disruption. The method is simple, quantitative, and recommended, especially in studies screening for bacteria not only with ß-glucosidase activity but also with high ß-glucosidase activity.

Necessity of purification during bacterial DNA extraction with environmental soils

Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for polymerase chain reaction (PCR) assays. Unfortunately the purification steps are also time and labor intensive. Therefore the necessity of DNA purification was re-visited and investigated for a variety of environmental soil samples that contained various amounts of PCR inhibitors. Bead beating and centrifugation was used as the baseline (without purification) method for DNA extraction. Its performance was compared with that of conventional DNA extraction kit (with purification). The necessity criteria for DNA purification were established with environmental soil samples. Using lysis conditions at 3000 rpm for 3 minutes with 0.1 mm glass beads, centrifugation time of 10 minutes and 1:10 dilution ratio, the baseline method outperformed conventional DNA extraction on cell seeded sand samples. Further investigation with PCR inhibitors (i.e., humic acids, clay, and magnesium [Mg]) showed that sand samples containing less than 10 μg/g humic acids and 70% clay may not require purifications. Interestingly, the inhibition pattern of Mg ion was different from other inhibitors due to the complexation interaction of Mg ion with DNA fragments. It was concluded that DNA extraction method without purification is suitable for soil samples that have less than 10 μg/g of humic acids, less than 70% clay content and less than 0.01% Mg ion content.

Prevalence of Complement-Mediated Cell Lysis-like Gene (sicG) in Streptococcus dysgalactiae subsp. equisimilis Isolates From Japan (2014–2016)

BACKGROUND: Streptococcus dysgalactiae subsp. equisimilis (SDSE; a β-hemolytic streptococcus of human or animal origin) infections are emerging worldwide. We evaluated the clonal distribution of complement-mediated cell lysis-like gene (sicG) among SDSE isolates from three central prefectures of Japan. METHODS: Group G/C β-hemolytic streptococci were collected from three institutions from April 2014 to March 2016. Fifty-five strains (52 from humans and three from animals) were identified as SDSE on the basis of 16S rRNA sequencing data.; they were obtained from 25 sterile (blood, joint fluid, and cerebrospinal fluid) and 30 non-sterile (skin-, respiratory tract-, and genitourinary tract-origin) samples. emm genotyping, multilocus sequence typing, sicG amplification/sequencing, and random amplified polymorphic DNA (RAPD) analysis of sicG-positive strains were performed. RESULTS: sicG was detected in 30.9% of the isolates (16 human and one canine) and the genes from the 16 human samples (blood, 10; open pus, 3; sputum, 2; throat swab, 1) and one canine sample (open pus) showed the same sequence pattern. All sicG-harboring isolates belonged to clonal complex (CC) 17, and the most prevalent emm type was stG6792 (82.4%). There was a significant association between sicG presence and the development of skin/soft tissue infections. CC17 isolates with sicG could be divided into three subtypes by RAPD analysis. CONCLUSIONS: CC17 SDSE harboring sicG might have spread into three closely-related prefectures in central Japan during 2014–2016. Clonal analysis of isolates from other areas might be needed to monitor potentially virulent strains in humans and animals.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Abstract Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

Production, purification and characterization of recombinant human antithrombin III by Saccharomyces cerevisiae

Background: Antithrombin III (ATIII) is a protein that inhibits abnormal blood clots (or coagulation) by breaking down thrombin and factor Xa. ATIII helps to keep a healthy balance between hemorrhage and coagulation. The present work demonstrated the production, purification and characterization of recombinant human antithrombin (rhAT) from yeast Saccharomyces cerevisiae BY4741 was demonstrated. After expression of rhAT by S. cerevisiae, the biomass and rhAT concentration were analyzed through fed-batch fermentation process. Results: In fed-batch fermentation, the biomass (maximum cell dry weight of 11.2 g/L) and rhAT concentration (312 mg/L) of the expressed rhAT were achieved at 84 h of cultivation time. The maximum cell lysis efficiency (99.89%) was found at 8 s sonication pulse and 7 mL lysis buffer volume. The rhAT protein solution was concentrated and partially purified using cross-flow filtration with the recovery yield and purity of 95 and 94%, respectively. The concentrated solution was further purified by the single step ion exchange chromatography with the recovery yield and purity of 55 and >98%, respectively. The purified rhAT was characterized by various analytical techniques, such as RP-HPLC, FT-IR, CD, SDS-PAGE, western blotting, and Liquid chromatography mass spectrometry (LC-MS) analysis. The biological activity of rhAT was analyzed as heparin cofactor to meet the therapeutic grade applications. Conclusions: The simple, cost-effective and economically viable nature of the process used in the present study for the production of rhAT will be highly beneficial for the healthcare sector. This may also be used to produce other value-added therapeutic recombinant proteins expressed in S. cerevisiae, with greater effectiveness and ease.

A Comparison of Cell Disruption Procedures for the Recovery of Intracellular Carotenoids from Sporobolomyces Ruberrimus H110.

Carotenoids are intracellular pigments produced by microorganisms, including some species of yeasts, in the stationary phase of growth by the secondary metabolic pathways. In the present study, different methods of Sporobolomyces ruberrimus H110 yeast cell lysis were evaluated with the objective of optimizing the recovery of intracellular pigments. Three extraction methods were used: vortex (glass beads and quartz stones), planetary mill (glass beads and quartz stones) and dimethyl sulfoxide. For each one of the lysis agents studied, factorial designs were developed considering as independent variables the agitation speed and lysis agent concentration. A central composite planning was defined considering as independent variables the lysis agent concentration and agitation speed, analyzing as response the estimated total number of extracted carotenoids. From the methods studied, a better extraction of total carotenoid (1.74 mg.g-1 of cells and of 1.57 mg.g-1 of cells) using the planetary mill method with 135 mg of glass beads or irregular quartz stones, with an agitation speed of 200 rpm. As to the cell lysis, the analysis indicated that the mechanical methods studied showed to be efficient in regards to cell laceration.

Beta-1,3 Glucanases e quitinases: aplicação na lise de leveduras e inibição de fungos / Beta-1,3 glucanases and chitinases: application in the yeast cell lysis and fungi inhibition

Objetivou-se, no presente trabalho, a aplicação de β-1,3 glucanases e quitinases da linhagem Cellulosimicrobium cellulans 191 na lise de leveduras e inibição de fungos, respectivamente. O delineamento experimental mostrou que as melhores condições para a lise de Saccharomyces cerevisiae KL-88 pela β-1,3 glucanase foi pH 6,5 e 35ºC. As células de leveduras incubadas por 10 h em frascos sem agitação mostraram-se mais susceptíveis à lise pela ação da enzima. Foi obtido maior lise da levedura quando a suspensão de células foi submetida ao tratamento com β-1,3 glucanase e cisteína 1mM. A enzima invertase intracelular ou ligada à célula de S. cerevisiae KL-88 e K. marxianus NCYC 587 foi extraída após tratamento da suspensão celular com β-1,3 glucanase, sendo que o tratamento prévio das leveduras com a enzima aumentou a susceptibilidade das células à lise com ultra-som. A preparação de quitinase foi capaz de formar halos de inibição de alguns fungos.

The aim of this work was the application of β-1,3 glucanases and chitinases by Cellulosimicrobium cellulans 191 strain on yeast cell lysis and fungi inhibition, respectively. The experimental design study showed that the best conditions to Saccharomyces cerevisiae KL-88 lysis by β-1,3 glucanase extract were pH 6,5 and 35ºC. This study also demonstrated that the yeast cells were more susceptible to lysis after 10 h of cultivation in flasks without agitation. Lysis activity was increased when S. cerevisiae KL-88 cell suspension was treated with β-1,3 glucanase and cystein 1mM. The enzyme invertase of S. cerevisiae KL-88 and Kluyveromyces marxianus NCYC 587 was extracted after treatment of cell suspension with β-1,3 glucanase and the previous treatment of yeasts with the enzyme, increased the susceptibility to lysis when ultrasonic treatment was used. The chitinase presented growth inhibition halos for some of the fungi.

Comparison of Clinical Effect Among Three Kinds of Hemapheresis / 中国医师杂志

Objective To compare the clinical outcome among white blood cell, platelet and red blood cell hemapheresis. Methods Thirty-seven patients with high blood cell count received hemapheresis for forty times by CS-3000 plus. Results After white blood cell hemapheresis, the peripheral white blood cell counts decreased from (231 52?355 56)?10 9/L to(140 64?230 85)?10 9/L(P

EVALUATION OF PROTEIN DETERMINATION IN URINE FOR GLOMERULAR HEMATURIA DIAGNOSIS / 中华肾脏病杂志

To study the affection of blood on protein determining in urine, different volumes of blood from healthy volunteers was added to urine samples of varied osmolatites. Specimens were analyzed for protein concentration by the method of 3% sulfosalicylic acid. Microscopic hematuria was not associated proteinuria. In hypertonic urines, the protein of gross hematuria is low (30mg/100ml for the urine with 3% RBC, 32. 4mg/100ml for the urine with 1% blood), while in iso and hypotonic urines gross hematuria produced marked proteinuria (225—1090mg/100ml). Urine protein electrophoreses identified hemoglobin as the responsible protein. The protein concentration in urine may he used to distinguish glomerular hematuria from nonglomerular hematuria.

Role of S gene product of bacteriophage lambda in host cell lysis.

Studies with the induced lysogens of λ S+R+, λS–R+, λS+R– and λS–R– phages have shown that while the S gene product is essential for the action of intracellular R gene product to release the periplasmic alkaline phosphatase in the presence of EDTA, the latter gene product can bring about this effect while acting on Escherichia coli cells from outside, in the absence of functional S gene product; chloroform, could help the intracellular R gene product in effecting bacterial lysis in the absence of S gene product. These result support the premise that the S gene product facilitates the R gene product in crossing the cytoplasmic membrane into the periplasmic space such that the latter can act on the peptidoglycan layer of the host cell thus causing both the release of alkaline phosphatase and cell lysis.