Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study

Background

Catheter-related infection (CRI) is one of the serious challenges in clinical practice. This preliminary clinical study aimed to examine whether next-generation sequencing (NGS) targeting 16S rDNA, which was PCR-amplified directly from the tip of a central venous catheter (CVC), can be used to identify causative pathogens in CRI, compared to the culture method.

Methods

Hospitalized patients, from whom a CVC had just been removed, were prospectively enrolled and divided into the CRI-suspected and routine removal groups. DNA was extracted from the sonication fluid of CVC specimens derived from patients. For analysis of bacterial composition by NGS, the V3–V4 fragments of bacterial 16S rDNA were PCR-amplified, followed by index PCR and paired-end sequencing on an Illumina MiSeq device. Conventional culture methods were also performed in the CRI-suspected group.

Results

Of CVCs collected from the 156 enrolled patients (114 men; mean age 65.6 years), a total of 14 specimens [nine out of 31 patients suspected with CRI and five out of 125 patients without infection symptoms (routine removal group)] were PCR-positive. In five patients with definite CRI, Staphylococcus was the most frequently detected genus by NGS (4/5 specimens), although no pathogens were detected by NGS in the one remaining specimen. The genera identified by NGS were consistent with those from conventional culture tests. There was high agreement between NGS and the culture method in the CRI-suspected group, with sensitivity and specificity values of 80.0% and 76.9%, respectively; meanwhile, the false-positive rate of NGS was as low as 4.0% in the routine removal group. Moreover, several genera, besides the genus identified by culture test, were detected in each patient with definite CRI and surgical site infection (SSI). Additionally, in one patient with SSI, Enterococcaceae were detected not only by NGS but also by abdominal abscess drainage culture.

Conclusions

NGS targeting 16S rDNA was able to analyze the bacterial composition of CVC specimens and detect causative pathogens in patients with CRI and was therefore suggested as a promising diagnostic tool for CRI.

     

Stabilization of Photosystem II (O(2) Evolution) of Spinach Chloroplasts by Radiation-induced Immobilization

Spinach chloroplasts were immobilized with vinyl monomers by radiation-induced polymerization at low temperature and stored in buffer containing bovine serum albumin. The lifetime of O₂ evolution activity in photosystem II was prolonged remarkably in immobilized chloroplasts. Thermostability of immobilized chloroplasts stored in buffer containing bovine serum albumin was far better than that of immobilized chloroplasts in pure buffer and that of intact chloroplasts. When immobilized chloroplasts were stored in buffer including polyethylene glycol, the lifetime of O₂ evolution activity was longer than for those stored in buffer containing bovine serum albumin.     

Cattle cDNA clone encoding a new allele of the MHC class II DQA1 gene

The nucleotide sequence data reported in this paper have been submitted to the DDBJ, EMBL, and GenBank nucleotide sequence databases and have been assigned the accession number D50454     

PHOTOSYNTHETIC PIGMENT COMPOSITION IN THE PRIMITIVE GREEN ALGA MESOSTIGMA VIRIDE (PRASINOPHYCEAE): PHYLOGENETIC AND EVOLUTIONARY IMPLICATIONS1

The photosynthetic pigment composition of Mesostigma viride Lauterborn, a primitive green alga, was determined. This alga contained chl a and b, lycopene, lutein, siphonaxanthin, γ‐carotene, β‐carotene, antheraxanthin, violaxanthin, neoxanthin, and two novel carotenoid fatty acid esters, siphonaxanthin C12:0 ester and siphonaxanthin C14:0 ester. The esters were saturated, whereas all previously identified siphonaxanthin and loroxanthin esters have been mono‐unsaturated (trans‐Δ2). Neoxanthin was the all‐trans form. This is the first such case detected in the chloroplasts of green plants. The 9′‐cis form of neoxanthin is believed to be universally present in the chloroplasts of green plants (Streptophyta and Chlorophyta) and is a precursor of abscisic acid. However, the 9′‐cis form was not found in M. viride. Based on these results, we discuss the phylogenetic implications and early evolution of the antenna pigment system in green plants.     

CHARACTERIZATION OF TWO UNIQUE CAROTENOID FATTY ACID ESTERS FROM PTEROSPERMA CRISTATUM (PRASINOPHYCEAE,CHLOROPHYTA)1

Carotenoid composition and spectroscopic characteristics were analyzed for Pterosperma cristatum Schiller, one of the most primitive known members of green algae. This alga contained a substantial amount of carotenoid esters, siphonaxanthin C14:1 trans‐Δ2 ester and 6′‐OH siphonaxanthin C14:1 trans‐Δ2 ester, but lacked lutein. This is the first report of carotenoid C14:1 trans‐Δ2 esters from phototrophic organisms. In vivo absorption spectra and excitation spectra of the cells revealed that these carotenoids absorbed blue‐green light and could transfer energy to chl a. These carotenoids were concluded to function as antenna pigments in P. cristatum.     

气候变化背景下江西省林火空间预测

林火是森林生态系统中重要的干扰因子之一,深刻地影响森林景观结构和功能。在全球气候化背景下,揭示气候变化对林火空间分布格局的影响,可为林火管理和防火资源分配提供科学指导。因此,基于江西省2001—2015年MODIS火影像数据(MCD14ML)和年均气温、年均降水量、植被、地形、人口密度、距道路距离、距居民点距离7个因子数据,利用增强回归树模型:(1)分析林火发生影响因子的相对重要性及其边际效应;(2)将GFDL-CM3和GISS-E2-R气候变化模式中的年均气温和年均降水量作为未来的气象数据,在3个温室气体排放量情景(RCP2.6、RCP4.5、RCP8.5)下,对2050年(2041—2060的平均值)和2070年(2061—2080的平均值)江西省林火分布进行预测,生成林火发生概率图。并采用受试者工作特征(ROC曲线)和混淆矩阵评估模型预测的精度。研究结果表明:(1)年均气温和海拔与江西省林火发生的相关性较强,年均降水量、居民点距离、人口密度、道路距离与林火发生的相关性较弱,但是与林火发生密切相关的如降水、风速等也应重点关注;(2)训练数据(70%)和验证数据(30%)的AUC值(ROC曲线下面积值)均为0.736,混淆矩阵对火点预测的正确率为67.8%,表明模型能够较好地预测研究区林火的发生;(3)在RCP8.5排放情景中林火发生的增幅最明显,其增幅较大的区域由赣南向赣北移动;(4)未来2050年和2070年林火发生与当前气候(2001—2015年)下相比,赣州市、鹰潭市的增幅较为明显,其他区域不明显。江西省各林业管理部门要加强林火高发区及潜在发生区的森林监测和管理,加大防火宣传力度,提升民众的森林防火意识。     

Nuclear export of phosphorylated galectin-3 regulates its antiapoptotic activity in response to chemotherapeutic drugs

Galectin-3 (Gal-3), a member of the beta-galactoside binding protein family containing the NWGR antideath motif of the Bcl-2 protein family, is involved in various aspects of cancer progression. Previously, it has been shown that the antiapoptotic activity of Gal-3 is regulated by the phosphorylation at Ser(6) by casein kinase 1 (CK1). Here we questioned how phosphorylation at Ser(6) regulates Gal-3 function. We have generated serine-to-alanine (S6A) and serine-to-glutamic acid (S6E) Gal-3 mutants and transfected them into the BT-549 human breast carcinoma cell line, which does not express Gal-3. BT-549 cell clones expressing wild-type (wt) and mutant Gal-3 were exposed to chemotherapeutic anticancer drugs. In response to the apoptotic insults, phosphorylated wt Gal-3 was exported from the nucleus to the cytoplasm and protected the BT-549 cells from drug-induced apoptosis while nonphosphorylated mutant Gal-3 neither was exported from the nucleus nor protected BT-549 cells from drug-induced apoptosis. Furthermore, leptomycin B, a nuclear export inhibitor, increased the cisplatin-induced apoptosis of Gal-3 expressing BT-549 cells. These results suggest that Ser(6) phosphoryaltion acts as a molecular switch for its cellular translocation from the nucleus to the cytoplasm and, as a result, regulates the antiapoptotic activity of Gal-3.     

Damage in DNA irradiated with 1.2 MHz ultrasound and its effect on template activity of DNA for RNA synthesis

When aqueous DNA solution was irradiated with 1.2 MHz continuous ultrasound in the presence of cysteamine, the number of ultrasound-induced double-strand breaks of DNA was not influenced, but the number of ultrasound-induced single-strand breaks of DNA was reduced to about one-fifth that of the irradiated control. When the effect of cysteamine on the template activity of the ultrasound-irradiated DNA was investigated, the cysteamine was found to exert a leveling effect on the linear decrease of the template activity against ultrasonic intensity. Since cysteamine was known as an effective radical scavenger, the results of the experiment were regarded to suggest that (1) the double-strand breaks were exclusively induced by the mechanical effect of ultrasound, (2) the majority of single-strand breaks were produced by water radicals arising from cavitation, (3) the initial part in the decrease of the template activity was due to the double-strand breaks arising from mechanical effect, and (4) the further decrease of the template activity depended mainly on the single-strand breaks arising from water radicals.     

Histology and tetracycline labeling of a single section of alveolar bone of first molars in the rat

We observed the histology and tetracycline (TC) labeling in a single frontal section of alveolar bone of upper first molars of adolescent rats. A single injection of TC was administered intraperitonealy in adolescent rats. After three weeks, the upper jaws were immersed rapidly in liquid nitrogen and sectioned. Five micrometer unfixed, undecalcified frozen sections were cut and observed by light and fluorescence microscopy. Frontal sections of the upper first molar area revealed that the structural relationships among the roots, the periodontal ligament and the alveolar bone, and also between the cervical enamel and the attachment epithelium were well preserved. The TC labeling lines in the sections were very clear and distinguished new bone from old bone. The brightness of the lines differed among regions. An analysis of the brightness in the same section suggested a difference in the bone forming activity at the time of injection.