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。     

基质金属蛋白酶-2/9敏感型可跨膜融合抗氧化酶的表达、纯化和表征北大核心CSCD

融合了跨膜肽的抗氧化酶可进入细胞,保护细胞免受放射损伤。然而跨膜肽的跨膜能力没有靶向性,其也可把抗氧化酶带入肿瘤细胞进而保护肿瘤细胞,降低放疗的效果。为此,根据多数肿瘤细胞微环境中存在活性基质金属蛋白酶(matrix metalloproteinase,MMP)-2或MMP-9的特点,在细胞跨膜肽R9与人铜、锌超氧化物歧化酶(superoxide dismutase 1,SOD1)和谷胱甘肽S-转移酶(glutathione S-transferase,GST)之间融合MMP-2/9的底物肽X,设计了融合蛋白GST-SOD1-X-R9。该蛋白在肿瘤微环境中可因MMP-2/9酶切底物肽X而失去跨膜肽,从而无法进入肿瘤细胞,进而只能进入正常细胞。全基因合成SOD1-X-R9序列,并将其插入原核表达载体pGEX-4T-1中,得到表达质粒,并实现了GST-SOD1-X-R9融合蛋白的可溶表达。GST-SOD1-X-R9经硫酸铵沉淀和GST亲和层析纯化,分子量约为47 kDa,与理论值一致。纯化的融合蛋白的SOD活性和GST活性分别为2954 U/mg和328 U/mg。GST-SOD1-X-R9的SOD活性或GST活性在生理条件下几乎没有变化。该融合蛋白在溶液中可被胶原酶Ⅳ部分水解。分别建立了2D和3D培养的HepG2细胞模型来检验肿瘤微环境中的MMP-2活力对该蛋白跨膜能力的影响。在2D培养模型中,HepG2的MMP-2活力极低,但在3D培养模型中,随着培养时间的增加,HepG2肿瘤球的体积变大,其胞外MMP-2活力也随之增强。GST-SOD1-X-R9在2D培养的HepG2细胞中具有和GST-SOD1-R9蛋白一样的跨膜效率,但在3D培养的HepG2细胞球中的跨膜能力大大降低。本研究为后续深入研究GST-SOD1-X-R9靶向防护正常细胞的氧化损伤效应奠定了基础。     

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.     

Effect of laterality discrimination on joint position sense and cervical range of motion in patients with chronic neck pain: a randomized single-blind clinical trial

Purpose: The main objective of the present study was to evaluate the effects of laterality discrimination training on neck joint position sense and cervical range of motion (ROM) in patients with chronic non-specific neck pain (NSCNP).

Materials and methods: Forty-eight patients with NSCNP were randomly assigned to the neck group (NG) that observed neck images or the foot group (FG) that observed foot images. Response time, response accuracy, cervical ROM, and joint position error (JPE) were the main variables. The secondary outcome measures included psychosocial variables.

Results: Differences between groups in the cervical ROM for flexion (p?=?.043) were obtained, being NG group the one which obtained greater values. NG showed an improvement in right rotation (p?=?.018) and a decrease in flexion was found in the FG (p?=?.039). In JPE, differences between groups were obtained in the left rotation (p?=?.021) and significant changes were found in the NG for flexion, extension, and left rotation movements (p?<?.05). Moderate associations were found between left and right accuracy regarding to post-intervention flexion and right rotation (r?=?0.46, r?=?0.41; p?<?.05) in NG.

Conclusion: Improvements in cervical range of motion and joint position sense are obtained after the performance of the laterality discrimination task of images of the neck but not the feet. Visualization of images of the painful region presents moderate correlations with the accuracy and response time in the movements of flexion and right rotation.     

Proteoglycan 4 deficiency protects against glucose intolerance and fatty liver disease in diet-induced obese mice

Objective

Proteoglycan 4 (Prg4) has emerged from human association studies as a possible factor contributing to weight gain, dyslipidemia and insulin resistance. In the current study, we investigated the causal role of Prg4 in controlling lipid and glucose metabolism in mice.

Modeling the vertical foliage distribution of an individual <Emphasis Type="Italic">Castanopsis cuspidata</Emphasis> (Thunb.) Schottky,a dominant broad-leaved tree in Japanese warm-temperate forest

The vertical foliage distribution of Castanopsis cuspidata (Thunb.) Schottky was examined in trees of various sizes to clarify its variation in relation to tree size and the light environment in a stand. As indices of these parameters, we analyzed crown social position (CSP: percent of stand height) and specific leaf area (SLA). The vertical foliage distribution of trees was expressed by a Weibull function. The variation in the vertical foliage distribution of C. cuspidata could be categorized into three types using crown social position and light environment. In the first type, leaves were concentrated to the top 20% of the tree; such trees are canopy trees that can receive full sunlight. The second type had a large relative crown depth and an asymmetric distribution with the maximum foliage located near the top of the tree; such trees are suppressed trees whose crowns do not receive sufficient light. The third type had a large relative crown depth and a symmetric distribution; such trees occur in high light environments, although their crowns are in the understory layer. The differences in the vertical foliage distribution are related to the strategies used to capture light. Multiple regression analysis showed that CSP and SLA at the top layer of the tree explained successive changes in the vertical foliage distribution. These results will contribute to scaling-up the vertical foliage distribution to the community level in pure stands of C. cuspidata using an individual-based model.     

Evaporative light scattering detection of pyrrolizidine alkaloids

A reverse-phase high-performance liquid chromatography method utilizing evaporative light scattering detection (ELSD) has been developed for the simultaneous detection of hepatotoxic pyrrolizidine alkaloids with and without chromophores, namely, riddelliine, riddelliine N-oxide, senecionine, senecionine N-oxide, seneciphylline, retrorsine, integerrimine, lasiocarpine and heliotrine. Pyrrolizidine alkaloids were detected in five plant extracts (Senecio spartioides, S. douglasii var. longilobus, S. jacobaea, S. intergerrimus var. exaltatus and Symphytum officinale). The detection of heliotrine (which does not contain a chromophore) was much improved by ELSD compared with photodiode array detection.     

Activation of hypersensitive cell death by pathogen-induced receptor-like protein kinases from <Emphasis Type="Italic">Arabidopsis</Emphasis>

In Arabidopsis, there is a family of receptor-like protein kinases (RLKs) containing novel cysteine-rich repeats in their extracellular domains. Genes encoding many of these cysteine-rich RLKs (CRKs) are induced by pathogen infection, suggesting a possible role in plant defense responses. We have previously generated Arabidopsis plants expressing four pathogen-regulated CRK genes (CRK5, 6, 10 and 11) under control of a steroid-inducible promoter and found that induced expression of CRK5, but not the other three CRK genes, triggered hypersensitive response-like cell death in transgenic plants. In the present study, we have analyzed the structural relationship of the CRK family and identified three CRKs (CRK4, 19 and 20) that are structurally closely related to CRK5. Genes encoding these three CRKs are all induced by salicylic acid and pathogen infection. Furthermore, induced expression of CRK4, 19and 20 all activates rapid cell death in transgenic plants. Thus, the activity of inducing rapid cell death is shared by these structurally closely related CRKs. We have also performed yeast two-hybrid screens and identified proteins that interact with the kinase domains of CRKs. One of the identified CRK-interacting proteins is the kinase-associated type 2C protein phospohatase known to interact with a number of other RLKs through its kinase-interacting FHA domain. Other CRK-interacting proteins include a second protein with a FHA domain and another type 2C protein phosphatase. Interactions of CRKs with these three proteins in vivo were demonstrated through co-immunoprecipitation. These CRK-interacting proteins may play roles in the regulation and signaling of CRKs.