A novel approach for tuberculosis diagnosis using exosomal DNA and droplet digital PCR.

OBJECTIVES: The rapid diagnosis of tuberculosis (TB) is important for patient treatment and infection control. Current molecular diagnostic techniques for TB have insufficient sensitivity to detect samples with low bacterial loads. The sensitivity of molecular testing depends on not only the performance of the assay technique but also the nucleic acid extraction method. Here, we present a novel approach using exosomal DNA (exoDNA) and droplet digital PCR (ddPCR) platforms to detect Mycobacterium tuberculosis DNA in clinical samples. METHODS: The ddPCR platform targeting IS6110 was evaluated in parallel using total DNA and exoDNA. The clinical performance of ddPCR method was assessed with 190 respiratory samples from patients with suspected pulmonary TB. RESULTS: Compared with mycobacterial culture, sensitivity and specificity of ddPCR were 61.5% (95% CI 44.6-76.6%) and 98.0% (95% CI 94.3-99.6%) using total DNA, and 76.9% (95% CI 60.7-88.9%) and 98.0% (95% CI 94.3-99.6%) using exoDNA, respectively. Among 15 culture-positive specimens with low concentrations of target molecules (2~99 positive droplets with exoDNA), only 53.3% (8/15), 46.7% (7/15), and 26.7% (4/15) of cases were detected using ddPCR with total DNA, real-time PCR with exoDNA, and real-time PCR with total DNA, respectively. DISCUSSION: Our platform using ddPCR and exoDNA has the potential to provide sensitive and accurate methodology for TB diagnosis.

Endophytic and endolichenic fungal diversity in maritime Antarctica based on cultured material and their evolutionary position among Dikarya.

Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts. They live asymptomatically within vascular plants, bryophytes and also in close association with algal photobionts inside lichen thalli. While endophytic diversity in land plants has been well studied, their diversity in lichens and bryophytes are poorly understood. Here, we compare the endolichenic and endophytic fungal communities isolated from lichens and bryophytes in the Barton Peninsula, King George Island, Antarctica. A total of 93 fungal isolates were collected from lichens and bryophytes. In order to determine their identities and evolutionary relationships, DNA sequences of the nuclear internal transcribed spacer (ITS), nuclear ribosomal small subunit (nuSSU), nuclear large subunit (nuLSU), and mitochondrial SSU (mtSSU) rDNA were obtained and protein coding markers of the two largest subunit of RNA polymerase II (RPB1 and RPB2) were generated. Multilocus phylogenetic analyses revealed that most of the fungal isolates were distributed in the following six classes in the phylum Ascomycota: Dothideomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Pezizomycetes and Sordariomycetes. For the first time we report the presence of subphylum Mortierellomycotina that may belong to an undescribed order in endophytic fungi. Taken together, our results imply that lichens and bryophytes provide similar niches and harbour a selection of these fungi, indicating generalists within the framework of evolutionary adaptation.

Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter.

A Gram-stain-negative, facultatively aerobic, cream-coloured, ovoid-shaped, non-motile and psychrotolerant bacterial strain, PAMC 27389T, was isolated from terrestrial soil collected on King George Island, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27389T belongs to the genus Pseudorhodobacter, sharing highest similarities with the type strains of Pseudorhodobacter wandonensis (96.9 %), Pseudorhodobacter antarcticus (96.8 %), Pseudorhodobacter ferrugineus (96.5 %) and Pseudorhodobacter aquimaris (95.4 %). Average nucleotide identity values between strain PAMC 27389T and the type strains of P. wandonensis, P. antarcticus, P. ferrugineus and P. aquimaris were 70.8, 70.9, 71.0 and 70.5 %, respectively and the genome-to-genome distances were 18.4-19.1 %, indicating PAMC 27389T is clearly distinguished from the most closely related Pseudorhodobacter species. The genomic DNA G+C content was 60.1 mol%. Strain PAMC 27389T grew at 0-37 °C (optimally at 15-20 °C), at pH 5.5-9.0 (optimally at pH 6.5-7.0) and in the presence of 0.5-3.0 % (w/v) sea salt (optimally with 0.5 %). It lacked bacteriochlorophyll a. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 1ω7c 11-methyl. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid, an unidentified lipid and three unidentified aminophospholipids. The major respiratory quinone was Q-10. Based on the phenotypic, chemotaxonomic and genomic data presented, we propose the name Pseudorhodobacter psychrotolerans sp. nov. with the type strain PAMC 27389T ( = KCTC 42640T = JCM 30764T).

Acquisition of extensive drug-resistant Pseudomonas aeruginosa among hospitalized patients: risk factors and resistance mechanisms to carbapenems.

Extensive drug-resistant Pseudomonas aeruginosa (XDRPA) strains, defined as resistant to all available antipseudomonal antibiotics, have been reported recently. This study aimed to investigate the risk factors for XDRPA acquisition by patients and the resistance mechanisms to carbapenems. From June to November 2007, XDRPA isolates were collected from patients in eight tertiary care hospitals. A case-control study was performed to determine factors associated with XDRPA acquisition. EDTA-imipenem disc synergy tests, and polymerase chain reaction amplification and sequencing were performed to detect the presence of metallo-ß-lactamases (MBLs). Risk factor analysis was performed for 33 patients. Mechanical ventilation [odds ratio (OR) 8.2, 95% confidence interval (CI) 1.3-52.2; P = 0.026] and APACHE II score (OR 1.2, 95% CI 1.0-1.3; P = 0.007) were identified as independent risk factors for XDRPA acquisition. Pulsed-field gel electrophoresis of XDRPA identified clonal epidemic isolates co-existing with sporadic isolates. Eight of 43 (19%) XDRPA isolates were shown to produce MBLs; four produced VIM-2 and four produced IMP-6. This study suggests a major role for mechanical ventilation in XDRPA acquisition. Moreover, pulsed-field gel electrophoresis identified a clonal epidemic within hospitals. Taken together, these results suggest that patient-to-patient transmission contributes to XDRPA acquisition in Korea.

Influence of oocyte donor and embryo recipient conditions on cloning efficiency in dogs.

To determine factors that affect the efficiency of dog cloning by somatic cell nuclear transfer, the present study was performed to investigate 1) the effects of surgical history (non-operated/operated) and parity (nullipara/multipara) on the recovery of in vivo canine oocytes; 2) the effects of surgical history and parity of recipients on the pregnancy and delivery; and 3) the effects of synchronization state (AA, advanced asynchrony; SY, synchrony; RA, retarded asynchrony) between oocytes donor and recipient on the pregnancy and delivery. Oocyte recovery rate was significantly higher in non-operated dogs compared to operated dogs (93.8 vs. 89.6%, P < 0.05) and not different between nulliparous dogs and multiparous dogs. Delivery rate was also significantly higher in non-operated dogs compared to operated dogs (2.8 vs. 1.0%, P < 0.05) and in nulliparous dogs than multiparous dogs (3.0 vs. 1.7%, P < 0.05). Even though SY showed increased pregnancy and delivery rate (20.0% and 3.0%) compared to AA (15.0% and 2.0%) and RA (0.0% and 0.0%), there was no significant difference. In conclusion, we recommend non-operated dogs as experimental dogs and nulliparous dogs as recipient dogs to increase delivery rate after transfer of somatic cell nuclear transferred embryos, but further study is needed to find out appropriate synchrony status at the transfer.

Effects of activin A on the in vitro development and mRNA expression of bovine embryos cultured in chemically-defined two-step culture medium.

The purpose of the present study was to evaluate the effects of activin A on the developmental competence of in vitro fertilized (IVF) bovine embryos derived from a two-step defined culture system (C1/C2 medium) during the early or later stages of embryo development. To evaluate the effects of activin A on transcriptional levels, we analysed genes related to blastocyst hatching and implantation and to activin signalling pathway in IVF embryos. Cumulus-oocyte complexes were matured for 22 h and fertilized in vitro. Presumptive zygotes were cultured in the presence or absence of activin A during early (0-120 h, C1) or later (120-192 h, C2) stages. Although the developmental competence of embryos cultured with activin A in C1 medium was not significantly different from their corresponding controls, development to blastocysts (22.4% vs 34.7%; p < 0.05) and the blastocyst hatching rate (9.3% vs 22.4%; p < 0.05) in C2 medium supplemented with 100 ng/ml activin A were significantly higher than in the control group. To evaluate the effect of activin A on transcription, the relative expression levels of genes related to blastocyst hatching and implantation (Na/K-ATPase, E-cad and Glut-1) as well as activin signalling pathway (ActRII, ActRIIB and Smad2) were analysed. Compared to control medium, gene expression of Na/K-ATPase, E-cad, Glut-1, ActRII and ActRIIB was increased in medium supplemented with activin A. In conclusion, this study suggests that activin A, during the later stage of in vitro bovine embryo development, can enhance in vitro development of embryos by increasing hatching rates and affecting expression levels of genes related to hatching and implantation in defined culture medium.

Effect of dimethyl sulfoxide on cell cycle synchronization of goldfish caudal fin derived fibroblasts cells.

Several studies have previously been conducted regarding cell cycle synchronization in mammalian somatic cells. However, limited work has been performed on the control of cell cycle stages in the somatic cells of fish. The aim of this study was to determine the cell cycle arresting effects of several dimethyl sulfoxide (DMSO) concentrations for different times on different cell cycle stages of goldfish caudal fin-derived fibroblasts. Results demonstrated that the cycling cells or control group (68.29%) yields significantly higher (p < 0.05) arrest in G0/G1 phase compared with the group treated for 24 h with different concentrations (0.5%, 1.0% or 1.5%) of DMSO (64.88%, 65.70%, 64.22% respectively). The cell cycle synchronization in the treatment of cells with 1.0% DMSO at 48 h (81.14%) was significantly higher than that in the groups treated for 24 h (76.82%) and the control group (77.90%). Observations showed that treatment of DMSO resulted in an increase in the proportion of cells at G0/G1 phase for 48 h of culture. However, high levels of apoptotic cells can be detected after 48 h of culture treated with 1% concentration of DMSO.

Birth of viable puppies derived from breeding cloned female dogs with a cloned male.

Since the establishment of production of viable cloned dogs by somatic cell nucleus transfer, great concern has been given to the reproductive abilities of these animals (Canis familiaris). Therefore, we investigated reproductive activity of cloned dogs by (1) performing sperm analysis using computer-assisted sperm analysis and early embryonic development, (2) assessing reproductive cycling by measuring serum progesterone (P4) levels and performing vaginal cytology, and (3) breeding cloned dogs using artificial insemination. Results showed that most parameters of sperm motility in a cloned male dog were within the reference range, and in vivo-matured oocytes from a noncloned female were successfully fertilized by spermatozoa from a cloned male dog and develop normally to the 8-cell stage. Three cloned female dogs displayed normal patterns of P4 levels and morphologic changes of the vaginal epithelium. Two cloned female dogs became pregnant using semen from a cloned male dog and successfully delivered 10 puppies by natural labor. In conclusion, these data demonstrated that both cloned male and female dogs are fertile, and their puppies are currently alive and healthy with normal growth patterns.

Improved efficiency of canine nucleus transfer using roscovitine-treated canine fibroblasts.

The aim of this study was to investigate whether roscovitine (the cyclin-dependent kinase 2 inhibitor) effectively induces synchronization of the donor cell cycle at G0/G1 and to examine the effect of donor cell cycle synchronization protocols on canine somatic cell nucleus transfer. Canine fibroblasts were obtained from skin biopsy cultures taken from a 7-yr-old retriever. The donor cell cycle was synchronized either by culturing cells to reach confluency or by treating cells with 15 microg/mL roscovitine for 24h. Cell cycle stages and apoptosis were analyzed by flow cytometry. After synchronization of the donor cell cycle, cells were placed with enucleated in vivo-matured dog oocytes, fused by electric stimulation, activated, and transferred into 18 naturally estrus-synchronized surrogates. There was no significant difference in cell cycle synchronization and apoptosis rates between the confluent and roscovitine groups. After transfer of reconstructed embryos, pregnancy was detected in three of nine surrogates that received cloned embryos reconstructed with roscovitine-treated cells, whereas only one of nine surrogates was pregnant after transfer of cloned embryos reconstructed with confluent cells. One pregnant female from the confluent cell group delivered one live and one dead pup, but the live one died within 5 days after birth. Three pregnant females from the roscovitine-treated cell group delivered eight live pups and one dead pup, and one of eight live pups died within 6 days after birth. In conclusion, the current results demonstrated that reconstructing embryos with roscovitine-treated cells resulted in increased efficiency of canine somatic cell nucleus transfer.

Surveillance of community-based reservoirs reveals the presence of CTX-M, imported AmpC, and OXA-30 beta-lactamases in urine isolates of Klebsiella pneumoniae and Escherichia coli in a U.S. community.

beta-Lactamases produced by urine isolates from patients in long-term care facilities (LTCFs), outpatient, clinics, and one hospital in a U.S. community were characterized. A total of 1.3% of all Escherichia coli and Klebsiella pneumoniae isolates collected from patients in 30 LTCFs and various outpatient clinics produced extended-spectrum beta-lactamases (ESBLs) and/or imported AmpC beta-lactamases.

Cloning endangered gray wolves (Canis lupus) from somatic cells collected postmortem.

The objective of the present study was to investigate whether nuclear transfer of postmortem wolf somatic cells into enucleated dog oocytes, is a feasible method to produce a cloned wolf. In vivo-matured oocytes (from domestic dogs) were enucleated and fused with somatic cells derived from culture of tissue obtained from a male gray wolf 6h after death. The reconstructed embryos were activated and transferred into the oviducts of naturally synchronous domestic bitches. Overall, 372 reconstructed embryos were transferred to 17 recipient dogs; four recipients (23.5%) were confirmed pregnant (ultrasonographically) 23-25 d after embryo transfer. One recipient spontaneously delivered two dead pups and three recipients delivered, by cesarean section, four cloned wolf pups, weighing 450, 190, 300, and 490g, respectively. The pup that weighed 190g died within 12h after birth. The six cloned wolf pups were genetically identical to the donor wolf, and their mitochondrial DNA originated from the oocyte donors. The three live wolf pups had a normal wolf karyotype (78, XY), and the amount of telomeric DNA, assessed by quantitative fluorescence in situ hybridization, was similar to, or lower than, that of the nuclear donor. In conclusion, the present study demonstrated the successful cloning of an endangered male gray wolf via interspecies transfer of somatic cells, isolated postmortem from a wolf, and transferred into enucleated dog oocytes. Therefore, somatic cell nuclear transfer has potential for preservation of canine species in extreme situations, including sudden death.

A cloned toy poodle produced from somatic cells derived from an aged female dog.

To date, dogs have been cloned with somatic cell nuclear transfer (SCNT), using donor cells derived from large-breed dogs 2 months to 3 years of age. The objective of the present study was to use SCNT to produce a small-breed dog from ear fibroblasts of an aged poodle, using large-breed oocyte donors and surrogate females, and to determine the origin of its mitochondrial DNA (mtDNA) and the length of its telomeres. Oocytes were derived from large-breed donors, matured in vivo, collected by flushing oviducts, and reconstructed with somatic cells derived from an aged (14-year-old) female toy poodle. Oocytes and donor cells were fused by electric stimuli, activated chemically, and transferred into the oviducts of large-breed recipient females. Overall, 358 activated couplets were surgically transferred into the oviducts of 20 recipient dogs. Two recipients became pregnant; only one maintained pregnancy to term, and a live puppy (weighing 190 g) was delivered by Caesarean section. The cloned poodle was phenotypically and genetically identical to the nuclear donor dog; however, its mtDNA was from the oocyte donor, and its mean telomere length was not significantly different from that of the nuclear donor. In summary, we demonstrated that a small-breed dog could be cloned by transferring activated couplets produced by fusion of somatic cells from a small-breed, aged donor female with enucleated in-vivo-matured oocytes of large-breed females, and transferred into the oviduct of large-breed recipient female dogs.

Improvement of canine somatic cell nuclear transfer procedure.

The purpose of the present study on canine somatic cell nuclear transfer (SCNT) was to evaluate the effects of fusion strength, type of activation, culture media and site of transfer on developmental potential of SCNT embryos. We also examined the potential of enucleated bovine oocytes to serve as cytoplast recipients of canine somatic cells. Firstly, we evaluated the morphological characteristics of in vivo-matured canine oocytes collected by retrograde flushing of the oviducts 72 h after ovulation. Secondly, the effectiveness of three electrical strengths (1.8, 2.3 and 3.3 kV/cm), used twice for 20 micros, on fusion of canine cytoplasts with somatic cells were compared. Then, we compared: (1) chemical versus electrical activation (a) after parthenogenetic activation or (b) after reconstruction of canine oocytes with somatic cells; (2) culture of resulting intergeneric (IG) embryos in either (a) mSOF or (b) TCM-199. The exposure time to 6-DMAP was standardized by using bovine oocytes reconstructed with canine somatic cells. Bovine oocytes were used for SCNT after a 22 h in vitro maturation interval. The fusion rate was significantly higher in the 3.3 kV/cm group than in the 1.8 and 2.3 kV/cm treatment groups. After parthenogenesis or SCNT with chemical activation, 3.4 and 5.8%, respectively, of the embryos developed to the morula stage, as compared to none of the embryos produced using electrical activation. Later developmental stages (8-16 cells) were transferred to the uterine horn of eight recipients, but no pregnancy was detected. However, IG cloned embryos (bovine cytoplast/canine somatic cell) were capable of in vitro blastocyst development. In vitro developmental competence of IG cloned embryos was improved after exposure to 6-DMAP for 4 h as compared to 0, 2 or 6h exposure, although the increase was not significantly different among culture media. In summary, for production of canine SCNT embryos, we recommend fusion at 3.3 kV/cm, chemical activation, culture in mSOF medium and transfer of presumptive zygotes to the oviduct of recipient animals. The feasibility of IG production of cloned canine embryos using bovine cytoplasts as recipient of canine somatic cells was demonstrated.

Birth of viable female dogs produced by somatic cell nuclear transfer.

Since the only viable cloned offspring born in dogs was a male, the purpose of the present study was to produce female puppies by somatic cell nuclear transfer (SCNT). Adult ear fibroblasts from a 2-month-old female Afghan hound were isolated and used as donor cells. In vivo-matured canine oocytes surgically collected (approximately 72h after ovulation) from the oviducts of 23 donors were used for SCNT. After removal of the cumulus cells, oocytes were enucleated, microinjected, fused with a donor cell, and activated. A total of 167 reconstructed SCNT embryos were surgically transferred (Day 0) into the oviducts of 12 recipient bitches (average 13.9 embryos/recipient, range 6-22) with spontaneous, synchronous estrous cycles. Three pregnancies were detected by ultrasonography on Day 23, maintained to term, and three healthy female puppies (520, 460, and 520g), were delivered by Caesarean section on Day 60. These puppies were phenotypically and genotypically identical to the cell donor. In conclusion, we have provided the first demonstration that female dogs can be produced by nuclear transfer of ear fibroblasts into enucleated canine oocytes.

Soluble microbial products (SMP) and soluble extracellular polymeric substances (EPS) from wastewater sludge.

Laspidou and Rittmann (Water Research 36:2711-2720, 2002) proposed that the soluble extracellular polymeric substances (EPS) are identical to soluble microbial products (SMP) in sludge liquor. In this paper, we compared the physicochemical characteristics of the SMP and soluble EPS from original and aerobically or anaerobically digested wastewater sludge. The surface charges, particle sizes, residual turbidities of polyaluminum chloride (PACl) coagulated supernatant, and chemical compositions of the SMP and soluble EPS containing suspensions were used as comparison index. Experimental results revealed that the particles in SMP and soluble EPS fractions extracted from original wastewater sludge, before and after digestion, were not identical in all physicochemical characteristics herein measured. The current test cannot support the proposal by Laspidou and Rittmann (Water Research 36:2711-2720, 2002) that SMP is identical to the soluble EPS from a wastewater sludge.

Metschnikowia koreensis sp. nov., a novel yeast species isolated from flowers in Korea.

A novel ascomycetous yeast was isolated from flowers of Lilium sp. and Ipomoea sp. in Korea. The name Metschnikowia koreensis sp. nov. (type strain SG99-34T = CBS 8854T = KCTC 7998T) is proposed for this novel species based on comparative sequence analyses of the D1/D2 domain of 26S rDNA and phenotypic characteristics.

In vitro anti-proliferative effect of 1,2,3,4,6-penta-O-galloyl-beta-D-glucose on human hepatocellular carcinoma cell line, SK-HEP-1 cells.

The root of Paeonia suffruticosa ANDREWS is an important Chinese crude drug used in many traditional prescriptions. 1,2,3,4,6-penta-O-galloyl-beta-D-glucose (PGG), a major component of this crude drug, was found to exhibit in vitro growth-inhibiting effect on human hepatocellular carcinoma cell line, SK-HEP-1 cells. The growth-inhibitory effect was related to the ability of PGG not only to cause a G(0)/G(1) phase arrest but also to suppress the activation of nuclear factor-kappa B. Neither apoptosis nor necrosis was observed in the cells treated with PGG. These findings suggest that PGG could be a candidate for developing a low-toxic anticancer agent.

[Differentiation of human hepatocarcinoma SMMC-7721 cells induced by HMBA].

In this paper, the effects of HMBA on the differentiation of human hepatocarcinoma cell line SMMC-7721 were investigated. After treated with 5 mmol/L HMBA, the proliferation of SMMC-7721 cells was inhibited remarkably, the cell growth inhibitory rate amounted to 64.14%, the cell mitotic index was declined by 53.88%. Light microscopy and transmission electron microscopy showed that the morphology and ultrastructure of the cells treated with HMBA undergone restorational alteration. Cytochemistry and immunocytochemistry assay revealed that the activities of gamma-GT declined and the levels of AFP and PCNA downregulated while the activity of TAT increased significantly after HMBA treatment. In the meantime, flow cytometry analysis showed that HMBA could arrest the cells in G0/G1 phase. The results showed that HMBA could effectively inhibit the proliferation, reverse the malignant morphology and ultrastructure, alter the levels of enzymes and antigens, arrest the cells in G0/G1, and induce the differentiation of human hepatocarcinoma SMMC-7721 cells in vitro.

Mistletoe lectin synergizes with paclitaxel in human SK-hep1 hepatocarcinoma cells.

The effect of mistletoe lectin I (ML-I), an inhibitor of ribosomal protein synthesis, on the in vitro cytotoxicity of a clinically important anticancer drug, paclitaxel, was studied on cultured human hepatocarcinoma SK-Hep1 cells using the microculture tetrazolium test. The interaction between these two agents was analyzed for true synergism using the ED50 isobologram. Synergism was observed in the simultaneous treatment of the cells with ML-I in combination with paclitaxel. In addition, 24-h exposure of the cells to a non-toxic dose of ML-I and lower toxic doses of paclitaxel in combination resulted in apoptotic cell death, as observed by agarose-gel electrophoresis of low-molecular-weight DNA and DNA flow cytometry. Thus, the results presented here indicate the potential clinical usefulness of ML-I combination therapy with paclitaxel.