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。     

Circannual changes in serum testosterone concentrations of adult and yearling woodchucks (Marmota monax)

Testicular volumes and serum testosterone concentrations were determined biweekly in 5 adult and 4 yearling woodchucks maintained indoors from December through August. Food and water were provided ad libitum except for 2 mo beginning at the winter solstice when feeding and lighting (12L:12D) supplemental to available natural light were discontinued. Temperatures fluctuated with outdoor temperatures greater than 4 degrees C. No significant hibernation occurred. Testes in adults were small in December (0.3-1.8 cm3), largest in February and March (3.5-5.6 cm3), and smallest in late June (0.1-0.5 cm3). Testosterone was basal in December (less than 0.6 ng/ml), maximal (3.4-6.6 ng/ml) between early January and late March, and minimal from April through August (less than 0.8 ng/ml). In yearlings, maximum testes volumes (1.6 cm3) and serum testosterone (0.9 +/- 0.2 ng/ml) were less, and occurred later, than in adults. Testosterone levels and testis volumes measured in newly captured woodchucks in March and April and again 2-3 mo later were generally similar to those of their laboratory counterparts. Thus, in woodchucks: annual cycles of testosterone production and of testes recrudescence and regression parallel each other with maxima during the short, late-winter breeding season; those cycles are not altered significantly by the absence of hibernation or the present conditions of captivity; and yearling males apparently are not an important part of the breeding population.     

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。     

Benthic foraminiferal population fluctuations related to anoxia: Santa Barbara Basin

The pore-water geochemistry and benthic foraminiferal assemblages of sediments from two slope sites and within the central portion of the Santa Barbara Basin were characterized between February 1988 and July 1989. The highest foraminiferal numerical densities (1197 cm^–3 as determined by an ATP assay) occurred at a slope site in June 1988 (550 m) in partially laminated sediments. In continuously laminated sediments from the central basin, foraminifera were found living (as determined by ATP assay) in October 1988 to depths of 4 cm, and specimens prepared for transmission electron microscopy were found with intact organelles to 3 cm, indicating their inhabitation of anoxic pore waters. Ultrastructural data from Nonionella stella is consistent with the hypothesis that this species can survive by anaerobic respiration. However, the benthic foraminifera appear unable to survive prolonged anoxia. The benthic foraminiferal population was completely dead in July 1989 when bottom water O₂ was undetectable.     

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.      

Purification and characterization of the 2-oxoglutarate dehydrogenase complex from Dictyostelium discoideum

The 2-oxoglutarate dehydrogenase complex was isolated from the cellular slime mould, Dictyostelium discoideum, and purified 113-fold. The enzyme exhibited Michaelis-Menten kinetics and the Km values for 2-oxoglutarate, CoA, and NAD were 1.0 mM, 0.002 mM, and 0.07 mM, respectively. The Ki value for succinyl-CoA was determined to be 0.004 mM and the Ki for NADH was 0.018 mM. AMP had positive effects whereas ATP had negative effects on the enzyme activity. The kinetic constants determined in this study and the reaction mechanism suggested can now be incorporated into a transition model of the tricarboxylic acid cycle during differentiation of D. discoideum.     

Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study

BackgroundThe standard of care treatment for muscle-invasive bladder cancer (MIBC) is radical cystectomy, which is typically preceded by neoadjuvant chemotherapy. However, the inability to assess minimal residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. Here, we sought to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis.Methods and findingsWe applied urine Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq), a targeted next-generation sequencing (NGS) method for detecting utDNA, to urine cell-free DNA (cfDNA) samples acquired between April 2019 and November 2020 on the day of curative-intent radical cystectomy from 42 patients with localized bladder cancer. The average age of patients was 69 years (range: 50 to 86), of whom 76% (32/42) were male, 64% (27/42) were smokers, and 76% (32/42) had a confirmed diagnosis of MIBC. Among MIBC patients, 59% (19/32) received neoadjuvant chemotherapy. utDNA variant calling was performed noninvasively without prior sequencing of tumor tissue. The overall utDNA level for each patient was represented by the non-silent mutation with the highest variant allele fraction after removing germline variants. Urine was similarly analyzed from 15 healthy adults. utDNA analysis revealed a median utDNA level of 0% in healthy adults and 2.4% in bladder cancer patients. When patients were classified as those who had residual disease detected in their surgical sample (n = 16) compared to those who achieved a pathologic complete response (pCR; n = 26), median utDNA levels were 4.3% vs. 0%, respectively (p = 0.002). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD detection was highly correlated with the absence of pCR (p < 0.001) with a sensitivity of 81% and specificity of 81%. Leave-one-out cross-validation applied to the prediction of pathologic response based on utDNA MRD detection in our cohort yielded a highly significant accuracy of 81% (p = 0.007). Moreover, utDNA MRD–positive patients exhibited significantly worse progression-free survival (PFS; HR = 7.4; 95% CI: 1.4–38.9; p = 0.02) compared to utDNA MRD–negative patients. Concordance between urine- and tumor-derived mutations, determined in 5 MIBC patients, was 85%. Tumor mutational burden (TMB) in utDNA MRD–positive patients was inferred from the number of non-silent mutations detected in urine cfDNA by applying a linear relationship derived from The Cancer Genome Atlas (TCGA) whole exome sequencing of 409 MIBC tumors. We suggest that about 58% of these patients with high inferred TMB might have been candidates for treatment with early immune checkpoint blockade. Study limitations included an analysis restricted only to single-nucleotide variants (SNVs), survival differences diminished by surgery, and a low number of DNA damage response (DRR) mutations detected after neoadjuvant chemotherapy at the MRD time point.ConclusionsutDNA MRD detection prior to curative-intent radical cystectomy for bladder cancer correlated significantly with pathologic response, which may help select patients for bladder-sparing treatment. utDNA MRD detection also correlated significantly with PFS. Furthermore, utDNA can be used to noninvasively infer TMB, which could facilitate personalized immunotherapy for bladder cancer in the future.

Pradeep S. Chauhan and colleagues, investigate a liquid biopsy solution via urine tumor DNA (utDNA) analysis to assess minimal residual disease in patients with muscle-invasive bladder cancer.