黄檗丛枝菌根真菌鉴定

目的：利用形态学特征与Nested-PCR技术鉴定黄檗丛枝菌根真菌。方法：采用酸性品红染色法挑选黄檗丛枝菌根。同时,利用湿筛法获得AM真菌孢子,进行形态学鉴定。运用Nested-PCR技术,对黄檗粗提DNA进行特异性扩增,采用blastn进行序列相似性比较。并构建系统进化树,确定侵染黄檗根系的AM真菌。结果：编号为HDAM-1的AM真菌孢子,形态特征与G．intraradices的特征描述一致。Nested-PCR检测到约455bp的目的片段,其序列与G．intraradices（DQ469118）相似性最高,达97．8％,有11个碱基的差异。系统进化树显示该序列在基于25S rDNA的进化树中与G．intraradices（DQ469118．1）处于同一分支,确定G．intraradices侵染黄檗根系。结论：将形态学特征与Nested-PCR技术相结合鉴定AM真菌,不仅简易、经济,而且能够提高研究结果的可靠性。     

半夏蛋白在小鼠早期妊娠子宫结合部位的检测

利用辣根过氧化物酶标记定位技术对半夏蛋白抗小鼠早期妊娠的作用原理进行了探讨。结果显示小鼠子宫内膜和腺管上皮以及胚胎外胚盘锥体部分呈现明显的酶棕显色颗粒,它们的产生能被未经酶标半夏蛋白所抑制。子宫内膜和胚胎的其他部分均未见与半夏蛋白有专一性的结合。本文对半夏蛋白的抗生育机理进行了简略的讨论。     

Bayesian adaptive sequence alignment algorithms

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.      

Quality of cardiovascular disease care in Ontario, Canada: missed opportunities for prevention - a cross sectional study

ABSTRACT: BACKGROUND: Primary care plays a key role in the prevention and management of cardiovascular disease (CVD). We examined primary care practice adherence to recommended care guidelines associated with the prevention and management of CVD for high risk patients. METHODS: We conducted a secondary analysis of cross-sectional baseline data collected from 84 primary care practices participating in a large quality improvement initiative in Eastern Ontario from 2008 to 2010. We collected medical chart data from 4,931 patients who either had, or were at high risk of developing CVD to study adherence rates to recommended guidelines for CVD care and to examine the proportion of patients at target for clinical markers such as blood pressure, lipid levels and hemoglobin A1c. RESULTS: Adherence to preventive care recommendations was poor. Less than 10% of high risk patients received a waistline measurement, half of the smokers received cessation advice, and 7.7% were referred to a smoking cessation program. Gaps in care exist for diabetes and kidney disease as 54.9% of patients with diabetes received recommended hemoglobin-A1c screenings, and only 55.8% received an albumin excretion test. Adherence rates to recommended guidelines for coronary artery disease, hypertension, and dyslipidemia were high (>75%); however <50% of patients were at target for blood pressure or LDL-cholesterol levels (37.1% and 49.7% respectively), and only 59.3% of patients with diabetes were at target for hemoglobin-A1c. CONCLUSIONS: There remain significant opportunities for primary care providers to engage high risk patients in prevention activities such as weight management and smoking cessation. Despite high adherence rates for hypertension, dyslipidemia, and coronary artery disease, a significant proportion of patients failed to meet treatment targets, highlighting the complexity of caring for people with multiple chronic conditions.Trial RegistrationNCT00574808.     

Release of tissue-specific proteins into coronary perfusate as a model for biomarker discovery in myocardial ischemia/reperfusion injury

Diagnosis of acute coronary syndromes is based on protein biomarkers, such as the cardiac troponins (cTnI/cTnT) and creatine kinase (CK-MB) that are released into the circulation. Biomarker discovery is focused on identifying very low abundance tissue-derived analytes from within albumin-rich plasma, in which the wide dynamic range of the native protein complement hinders classical proteomic investigations. We employed an ex vivo rabbit model of myocardial ischemia/reperfusion (I/R) injury using Langendorff buffer perfusion. Nonrecirculating perfusate was collected over a temporal profile of 60 min reperfusion following brief, reversible ischemia (15 min; 15I/60R) for comparison with irreversible I/R (60I/60R). Perfusate proteins were separated using two-dimensional gel electrophoresis (2-DE) and identified by mass spectrometry (MS), revealing 26 tissue-specific proteins released during reperfusion post-15I. Proteins released during irreversible I/R (60I/60R) were profiled using gel-based (2-DE and one-dimensional gel electrophoresis coupled to liquid chromatography and tandem mass spectrometry; geLC-MS) and gel-free (LC-MS/MS) methods. A total of 192 tissue-specific proteins were identified during reperfusion post-60I. Identified proteins included those previously associated with I/R (myoglobin, CK-MB, cTnI, and cTnT), in addition to examples currently under investigation in large cohort studies (heart-type fatty acid binding protein; FABPH). The postischemic release profile of a novel cardiac-specific protein, cysteine and glycine-rich protein 3 (Csrp3; cardiac LIM domain protein) was validated by Western blot analysis. We also identified Csrp3 in serum from 6 of 8 patients postreperfusion following acute myocardial infarction. These studies indicate that animal modeling of biomarker release using ex vivo buffer perfused tissue to limit the presence of obfuscating plasma proteins may identify candidates for further study in humans.     

Monoclonal TCR-redirected tumor cell killing

T cell immunity can potentially eradicate malignant cells and lead to clinical remission in a minority of patients with cancer. In the majority of these individuals, however, there is a failure of the specific T cell receptor (TCR)–mediated immune recognition and activation process. Here we describe the engineering and characterization of new reagents termed immune-mobilizing monoclonal TCRs against cancer (ImmTACs). Four such ImmTACs, each comprising a distinct tumor-associated epitope-specific monoclonal TCR with picomolar affinity fused to a humanized cluster of differentiation 3 (CD3)-specific single-chain antibody fragment (scFv), effectively redirected T cells to kill cancer cells expressing extremely low surface epitope densities. Furthermore, these reagents potently suppressed tumor growth in vivo. Thus, ImmTACs overcome immune tolerance to cancer and represent a new approach to tumor immunotherapy.     

Echinometra sea urchins acclimatized to elevated pCO2 at volcanic vents outperform those under present‐day pCO2 conditions

Rising atmospheric CO₂ concentrations will significantly reduce ocean pH during the 21st century (ocean acidification, OA). This may hamper calcification in marine organisms such as corals and echinoderms, as shown in many laboratory‐based experiments. Sea urchins are considered highly vulnerable to OA. We studied an Echinometra species on natural volcanic CO₂ vents in Papua New Guinea, where they are CO₂‐acclimatized and also subjected to secondary ecological changes from elevated CO₂. Near the vent site, the urchins experienced large daily variations in pH (>1 unit) and pCO₂ (>2000 ppm) and average pH values (pH_T 7.73) much below those expected under the most pessimistic future emission scenarios. Growth was measured over a 17‐month period using tetracycline tagging of the calcareous feeding lanterns. Average‐sized urchins grew more than twice as fast at the vent compared with those at an adjacent control site and assumed larger sizes at the vent compared to the control site and two other sites at another reef near‐by. A small reduction in gonad weight was detected at the vents, but no differences in mortality, respiration, or degree of test calcification were detected between urchins from vent and control populations. Thus, urchins did not only persist but actually ‘thrived’ under extreme CO₂ conditions. We suggest an ecological basis for this response: Increased algal productivity under increased pCO₂ provided more food at the vent, resulting in higher growth rates. The wider implication of our observation is that laboratory studies on non‐acclimatized specimens, which typically do not consider ecological changes, can lead to erroneous conclusions on responses to global change.     

Improving the quality of protein structure models by selecting from alignment alternatives

Background  

In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection.