Changes in retention behavior of fluorescently labeled proteins during ion-exchange chromatography caused by different protein surface labeling positions

Confocal laser scanning microscopy (CLSM) is a method allowing in situ visualization of protein transport in porous chromatography resins. CLSM requires labeling a protein with a fluorescent probe. Recent work has shown that conjugation of the protein with fluorescent probes can lead to significant changes in the retention time of the protein-dye conjugate with respect to the unlabeled protein. In this study, we show that common labeling procedures result in a heterogeneous mixture of different variants and that attachment location of the fluorescent probe on the protein surface can have a strong effect on the retention of protein-dye conjugate. Lysozyme was labeled with Cy5 and BODIPY-FL succinimidyl esters, followed by chromatographic separation of the different lysozyme-dye conjugates and subsequent determination of the label position using MALDI-TOF-MS. Finally, homogenously labeled lysozyme-dye conjugates were used in CLSM experimentation and compared to published results arising from heterogeneously labeled feedstocks. The results confirm that the attachment location of the fluorescent probe has a strong effect on chromatographic retention behavior. When addressing the binding affinities of the different labeled protein fractions, it was found that native lysozyme was able to displace lysozyme-dye conjugates when the fluorescent label was attached to lysine-33, but not when attached to lysine-97. Finally, it could be shown that when superimposing the single profiles of the three major fractions obtained during a labeling procedure a qualitative picture of the net profile is obtained.     

Ecological application of wavelet analysis in the scaling of spatial distribution patterns of Ceratoides ewersmanniana

Ecological experiments are usually conducted on small scales, but the ecological and environmental issues are usually on large scales. Hence, there is a clear need of scaling. Namely, when we deal with patterns and processes on larger scales, a special connection needs to be established on the small scales that we are familiar with. Here we presented a wavelet analysis method that could build relationships between spatial distribution patterns on different scales. With this method, we also studied how spatial heterogeneity and distribution patterns changed with the scale. We investigated the distribution and the habitat of C. ewersmanniana in two plots (200 m × 200 m; the distance between these two plots is 15 km) at Mosuowan desert. The results demonstrated that spatial heterogeneity and distribution patterns were incorporated into larger scales when the wavelet scale varied from one (5 m) to four (20 m). However, if the wavelet scale was above five (25 m), the spatial distribution patterns varied placidly, the oscillation frequency of landforms stabilized at 110 m, and the dynamic quantity period of C. ewersmanniana stabilized at 115–125 m. We also identified signal mutation points with wavelet analysis and verified the heterogeneity degree of local space with position variance. We found that position variance decomposed the distribution patterns on large scales into small sampling plots, and the position with the largest variance also had the strongest heterogeneity. In a word, the wavelet analysis method could scale-up spatial distribution patterns and habitat heterogeneity. With this method and other methods derived from this one, such as wavelet scale, wavelet variance, position variance and extremely direct-viewing graphs, wavelet analysis could be widely applied in solving the scaling problem in ecological and environmental studies.     

Beta结构氨基酸支持度分析的研究

蛋白质空间结构的分析与预测已经成为现今分子生物学和生物信息学的重要研究课题之一。虽然引入了3D-profile,人工神经网络,遗传算法等复杂的模型或算法,并获得了相对较高的准确率,但是却很难对所得到的结果进行解释,且不易发现其中的生物学规律。而相应地,氨基酸序列所隐含的蛋白质结构信息,生物学和数学意义才应是我们所需探寻的重点。因此我们从分析构成特定二级结构的氨基酸序列着手,引入涉及关联规则的支持度S来计算特殊位点处氨基酸的贡献率,以期发现其中的隐含信息,并获得了相应的数据信息矩阵。通过分析二级结构的支持度,不仅得到了各氨基酸位于不同位点时相对于Beta结构的强弱作用关系,还发现了脯氨酸的特殊作用和相对于Beta结构的成核性。     

Automated work-flow for processing high-resolution direct infusion electrospray ionization mass spectral fingerprints

The use of mass spectrometry (MS) is pivotal in analyses of the metabolome and presents a major challenge for subsequent data processing. While the last few years have given new high performance instruments, there has not been a comparable development in data processing. In this paper we discuss an automated data processing pipeline to compare large numbers of fingerprint spectra from direct infusion experiments analyzed by high resolution MS. We describe some of the intriguing problems that have to be addressed, starting with the conversion and pre-processing of the raw data to the final data analysis. Illustrated on the direct infusion analysis (ESI-TOF-MS) of complex mixtures the method exploits the full quality of the high-resolution present in the mass spectra. Although the method is illustrated as a new library search method for high resolution MS, we demonstrate that the output of the preprocessing is applicable to cluster-, discriminant analysis, and related multivariate methods applied directly to mass spectra from direct infusion analysis of crude extracts. This is done to find the relationship between several terverticillate Penicillium species and identify the ions responsible for the segregation.     

不同体位下输尿管硬镜对输尿管上段结石患者的疗效及安全性分析

摘要 目的：对比不同体位下输尿管硬镜对输尿管上段结石患者的疗效及安全性。方法：2018年8月到2021年1月选择在本院诊治的输尿管上段结石的患者88例作为研究对象,根据随机信封抽签1:1原则把患者分为头高臀低组与水平位组各44例。所有患者均给予输尿管硬镜手术治疗,头高臀低组给予头高臀低截石位,水平位组给予水平截石位,记录与随访疗效及安全性。结果：所有患者顺利完成手术,头高臀低组碎石时间等围手术指标少于水平位组（P<0.05）。头高臀低组术后14 d的总有效率为97.7 %,高于水平位组的86.4 %（P<0.05）。头高臀低组术后14 d的假道形成、输尿管穿孔、粘膜撕脱、感染等总发生率为4.5 %,低于水平位组的25.0 %（P<0.05）。两组术后14 d的血清同型半胱氨酸（Hcy）和β2-微球蛋白（β2-MG）含量较术前1 d低（P<0.05）,头高臀低组低于水平位组（P<0.05）。所有患者术后随访6个月,头高臀低组的复发率为2.3 %,低于水平位组的13.6 %（P<0.05）。结论：相对水平截石位,头高臀低截石位在输尿管上段结石患者输尿管硬镜手术患者的应用能提高总体治疗效果,促进患者康复,也可降低血清同型半胱氨酸和β2-微球蛋白,减少并发症的发生,降低复发率。     

重症肺炎患儿俯卧位与仰卧位机械通气的临床效果比较及其脱机结局的影响因素分析

摘要 目的：比较重症肺炎患儿俯卧位与仰卧位机械通气的临床效果,并分析其脱机结局的影响因素。方法：选择2020年5月~2021年12月期间在我院重症监护室（ICU）住院的重症肺炎患儿120例作为研究对象。根据机械通气体位方式的不同将患儿分为仰卧组（n=52）和俯卧组（n=68）,对比仰卧组、俯卧组的临床症状改善时间和血气分析指标[动脉血氧分压（PaO₂）、动脉血二氧化碳分压（PaCO₂）、平均动脉压（MAP）]。记录仰卧组、俯卧组的死亡例数、脱机成功和脱机失败例数,计算死亡率、脱机失败发生率。采用单因素及多因素Logistic回归分析脱机失败的影响因素。结果：俯卧组的发热消失时间、肺部啰音消失时间、呼吸改善时间短于仰卧组（P<0.05）。两组治疗5 d后 PaO₂、MAP较治疗前升高,PaCO₂较治疗前下降（P<0.05）;俯卧组的PaO₂、MAP高于仰卧组,PaCO2低于仰卧组（P<0.05）。两组患儿死亡率组间对比未见统计学差异（P>0.05）。俯卧组的脱机失败率低于仰卧组（P<0.05）。在120例患儿中,死亡7例,根据重症肺炎患儿脱机结局将剩余113例分为脱机成功组（n=72）和脱机失败组（n=41）,脱机失败组、脱机成功组在年龄、急性生理与慢性健康评分系统II（APACHE II）评分、病程、先天性病史、D-二聚体（D-D）、白蛋白（ALB）、血乳酸、脑尿钠肽（BNP）方面对比有统计学差异（P<0.05）。多因素Logistic回归分析结果显示：年龄偏小、APACHE II评分偏高、D-D偏高、ALB偏低、先天性病史均是重症肺炎患儿脱机结局的影响因素（P<0.05）。结论：与仰卧位相比,俯卧位机械通气用于重症肺炎患儿可获得更好的临床效果和脱机成功率,且患儿的脱机结局受到年龄、APACHE II评分、D-D、ALB、先天性病史的影响。     

基于卷积神经网络的大肠杆菌启动子预测

目的 基于位点特异性打分矩阵（position-specific scoring matrices,PSSM）的预测模型已经取得了良好的效果,基于PSSM的各种优化方法也在不断发展,但准确率相对较低,为了进一步提高预测准确率,本文基于卷积神经网络（convolutional neural networks,CNN）算法做了进一步研究。方法 采用PSSM将启动子序列处理成数值矩阵,通过CNN算法进行分类。大肠杆菌K-12（Escherichia coli K-12,E.coli K-12,下文简称大肠杆菌）的Sigma38、Sigma54和Sigma70 3种启动子序列被作为正集,编码（Coding）区和非编码（Non-coding）区的序列为负集。结果 在预测大肠杆菌启动子的二分类中,准确率达到99%,启动子预测的成功率接近100%;在对Sigma38、Sigma54、Sigma70 3种启动子的三分类中,预测准确率为98%,并且针对每一种序列的预测准确率均可以达到98%以上。最后,本文以Sigma38、Sigma54、Sigma70 3种启动子分别和Coding区或者Non-coding区序列做四分类,预测得到的准确性为0.98,对3种Sigma启动子均衡样本的十交叉检验预测精度均可以达到0.95以上,海明距离为0.016,Kappa系数为0.97。结论 相较于支持向量机（support vector machine,SVM）等其他分类算法,CNN分类算法更具优势,并且基于CNN的分类优势,编码方式亦可以得到简化。     

The PDZ-GEF Gef26 regulates synapse development and function via FasII and Rap1 at the Drosophila neuromuscular junction

Guanine nucleotide exchange factors (GEFs) are essential for small G proteins to activate their downstream signaling pathways, which are involved in morphogenesis, cell adhesion, and migration. Mutants of Gef26, a PDZ-GEF (PDZ domain-containing guanine nucleotide exchange factor) in Drosophila, exhibit strong defects in wings, eyes, and the reproductive and nervous systems. However, the precise roles of Gef26 in development remain unclear. In the present study, we analyzed the role of Gef26 in synaptic development and function. We identified significant decreases in bouton number and branch length at larval neuromuscular junctions (NMJs) in Gef26 mutants, and these defects were fully rescued by restoring Gef26 expression, indicating that Gef26 plays an important role in NMJ morphogenesis. In addition to the observed defects in NMJ morphology, electrophysiological analyses revealed functional defects at NMJs, and locomotor deficiency appeared in Gef26 mutant larvae. Furthermore, Gef26 regulated NMJ morphogenesis by regulating the level of synaptic Fasciclin II (FasII), a well-studied cell adhesion molecule that functions in NMJ development and remodeling. Finally, our data demonstrate that Gef26-specific small G protein Rap1 worked downstream of Gef26 to regulate the level of FasII at NMJs, possibly through a βPS integrin-mediated signaling pathway. Taken together, our findings define a novel role of Gef26 in regulating NMJ development and function.     

Effect of stochastic resonance on proprioception and kinesthesia in anterior cruciate ligament reconstructed patients

Low amplitude mechanical noise vibration has been shown to improve somatosensory acuity in various clinical groups with comparable deficiencies through a phenomenon known as Stochastic Resonance (SR). This technology showed promising outcomes in improving somatosensory acuity in other clinical patients (e.g., Parkinson’s disease and osteoarthritis). Some degree of chronic somatosensory deficiency in the knee has been reported following anterior cruciate ligament (ACL) reconstruction surgery. In this study, the effect of the SR phenomenon on improving knee somatosensory acuity (proprioception and kinesthesia) in female ACL reconstructed (ACLR) participants (n = 19) was tested at three months post-surgery, and the results were compared to healthy controls (n = 28). Proprioception was quantified by the measure of joint position sense (JPS) and kinesthesia with the threshold to detection of passive movement (TDPM).The results based on the statistical analysis demonstrated an overall difference between the somatosensory acuity in the ACLR limb compared to healthy controls (p = 0.007). A larger TDPM was observed in the ACLR limb compared to the healthy controls (p = 0.002). However, the JPS between the ACLR and healthy limbs were not statistically significantly different (p = 0.365). SR significantly improved JPS (p = 0.006) while the effect was more pronounced in the ACLR cohort. The effect on the TDPM did not reach statistical significance (p = 0.681) in either group.In conclusion, deficient kinesthesia in the ACLR limb was observed at three months post-surgery. Also, the positive effects of SR on somatosensory acuity in the ACL reconstructed group warrant further investigation into the use of this phenomenon to improve proprioception in ACLR and healthy groups.     

Fish larvae distribution among different habitats in coastal East Africa

Fish larvae abundances, diversity and trophic position across shallow seagrass, coral reef and open water habitats were examined to characterize their distribution in coastal East Africa. Larvae were identified to family and analysed for abundance differences between sites and habitats, trophic level using stable-isotope analysis and parental spawning mode. Abundances differed greatly between sites with the highest numbers of larvae occurring in the open-water and seagrass habitats. Larval fish diversity was high across habitats with 51 families identified with small differences between sites and among habitats. Notably, larvae of abundant large herbivorous fishes present in reef and seagrass habitats were almost completely absent at all sampling locations. In the seagrass, demersal spawned larvae were more abundant compared with the reef and open-water habitats. Stable-isotope analysis revealed that fish larvae have a varied diet, occupying trophic level two to three and utilizing planktonic prey. This study offers new insights into distributional aspects of fish larvae along the East African coast where such information is sparse.