An Improved Computational Prediction Model for Lysine Succinylation Sites Mapping on Homo sapiens by Fusing Three Sequence Encoding Schemes with the Random Forest Classifier

Background Lysine succinylation is one of the reversible protein post-translational modifications (PTMs), which regulate the structure and function of proteins. It plays a significant role in various cellular physiologies including some diseases of human as well as many other organisms. The accurate identification of succinylation site is essential to understand the various biological functions and drug development.Methods In this study, we developed an improved method to predict lysine succinylation sites mapping on Homo sapiens by the fusion of three encoding schemes such as binary, the composition of k-spaced amino acid pairs (CKSAAP) and amino acid composition (AAC) with the random forest (RF) classifier. The prediction performance of the proposed random forest (RF) based on the fusion model in a comparison of other candidates was investigated by using 20-fold cross-validation (CV) and two independent test datasets were collected from two different sources.Results The CV results showed that the proposed predictor achieves the highest scores of sensitivity (SN) as 0.800, specificity (SP) as 0.902, accuracy (ACC) as 0.919, Mathew correlation coefficient (MCC) as 0.766 and partial AUC (pAUC) as 0.163 at a false-positive rate (FPR) = 0.10 and area under the ROC curve (AUC) as 0.958. It achieved the highest performance scores of SN as 0.811, SP as 0.902, ACC as 0.891, MCC as 0.629 and pAUC as 0.139 and AUC as 0.921 for the independent test protein set-1 and SN as 0.772, SP as 0.901, ACC as 0.836, MCC as 0.677 and pAUC as 0.141 at FPR = 0.10 and AUC as 0.923 for the independent test protein set-2. It also outperformed all the other existing prediction models.Conclusion The prediction performances as discussed in this article recommend that the proposed method might be a useful and encouraging computational resource for lysine succinylation site prediction in the case of human population.     

Prion protein modifies TGF-beta induced signal transduction

Members of the transforming growth factor-beta (TGF-beta) superfamily regulate a multitude of cellular processes as well as the expression of various proteins such as, e.g., matrix metalloproteinases (MMPs). These endopeptidases selectively degrade components of the extracellular matrix as well as non-matrix substrates like growth factors and cell surface receptors. MMPs are activated during embryonic development, morphogenesis, and tissue resorption/remodeling as well as in pathological conditions such as deranged wound healing and cancer metastasis. In this report we demonstrate that over-expression of cellular prion protein in mouse mammary gland epithelial cells is able to modulate TGF-beta induced signal transduction leading to a synergistic increase of secreted MMP-2 activity. This correlates with elevated substrate detachment of cells grown as an epithelial monolayer as well as interfering with morphogenesis of cells cultured in a three-dimensional collagen type I matrix.     

中国小腹茧蜂属二新种记述(膜翅目,茧蜂科,小腹茧蜂亚科)

记述了采自黑龙江、吉林、辽宁和湖北省小腹茧蜂属M.icrogaster Latreille,18042新种,短管小腹茧蜂M.breviterebrae sp．nov．和长距小腹茧蜂M．longicalcar sp．nov．。短管小腹茧蜂M.breviterebrae sp．nov．(♀)与M．grandis相似,但以下特征可以区别：1)翅痣下方具暗斑(后者无);2)触角端前节长为宽的1．2倍(后者为2倍);3)头顶光滑(后者具皱纹);4)腹部第3背板光滑(后者具皱状刻点);5)后足胫节黑色(后者红黄色)。采自黑龙江镜泊湖、吉林长春、辽宁(阜新、大连、沈阳)。长距小腹茧蜂M．longicalcar sp．nov．(♀)与短管小腹茧蜂M.breviterebrae sp．nov．相似,但以下特征可以区别：1)1—RS脉长为1—M脉1／2(后者为1／3);2)r脉与翅痣宽等长(后者明显短于翅痣宽);3)后足胫节内距长为基跗节6／7(后者为1／2);4)产卵管鞘长为后足胫节1／2(后者为1／3);5)前后单眼间距与单眼直径等长(后者短于单眼直径)。采自湖北房县。本文附中国小腹茧蜂属分种检索表。模式标本均保存在浙江大学植保系寄生蜂标本室。     

ROS and oncogenesis with special reference to EMT and stemness

Elevation of the level of intracellular reactive oxygen species (ROS) has immense implication in the biological system. On the one hand, ROS promote the signaling cascades for the maintenance of normal physiological functions, the phenomenon referred to as redox biology, and on the other hand increased ROS can cause damages to the cellular macromolecules as well as genetic material, the process known as oxidative stress. Oxidative stress acts as an etiological factor for wide varieties of pathologies, cancer being one of them. ROS is regarded as a “double-edged sword” with respect to oncogenesis. It can suppress as well as promote the malignant progression depending on the type of signaling pathway it uses. Moreover, the attribution of ROS in promoting phenotypic plasticity as well as acquisition of stemness during neoplasia has become a wide area of research. The current review discussed all the aspects of ROS in the perspective of tumor biology with special reference to epithelial-mesenchymal transition (EMT) and cancer stem cells.     

Air Pollution: Involvement of Oxygen Radicals (A Mini Review)

In the past decades air pollution has increased worldwide. We also gained more insight into the complex interactions between different air pollutants in the atmosphere as well as their effects on living cells and organisms. It also has been unequivocally shown by several groups in different countries that oxy radicals play an outstanding role in the interconversion of air pollutants as well as during the manifestation of toxic effects. Not only living systems are affected by air pollutants, but also inorganic systems such as buildings and sculptures. In the following overview the most important reactions occuring in the atmosphere as well as effects of oxidative gaseous compounds and particles such as diesel soot and asbestos will be discussed.     

Ethnobotany of Ghalegay, District Swat, Pakistan

Ethnobotanical study of plants revealed that the local community of Ghalegy, District Swat, invariably uses 126 species of 59 families for various purposes. Based on their traditional local uses, fifty-seven species （45.2%） were classifted as medicinal, forty-seven as fire wood （37.3 % ）, forty-five as forage （35.7 % ）, twenty-eight as honey bee species （22.2%）, twenty-seven as vegetable species （21.4%）, 25 as edible fruits （14 wild and llcultivated）, thirteen as timberwood （10.3%）, twelve as ornamental （9.5%）, eleven as furniture wood, ten as shelter and thatch makers （7.9%）, ten as fencing （7.9%）, five as poisonous （4%）, four as religious/superstitious species, three species used in making hand sticks and wooden tools （2.4%）, three as utensil cleaner species （2.4%）, three as evil repellent and one as fish poisoning species. The area is in plant resources and traditional knowledge but it needs ecological management for its sustainability.     

Get a grip: Podosomes as potential players in phagocytosis

Podosomes have been known for several decades as micron-sized, F-actin-rich structures that play a pivotal role in cell migration and invasion, as they are able to mediate both cell-matrix attachment as well as extracellular matrix degradation. Particularly in monocytic cells, podosomes have been shown to fulfill a variety of additional functions such as sensing of substrate rigidity and topography, or cell-cell fusion. Increasing evidence now points to the involvement of podosome-like structures also during phagocytosis by immune cells such as macrophages, dendritic cells, and neutrophils. Here, we compare the different cell models and experimental set ups where “phagocytic podosomes” have been described. We also discuss the composition and architecture of these structures, their potential involvement in mechanosensing and particle disruption, as well as the pros and cons for addressing them as bona fide podosomes.     

Genetic networks regulated by ASYMMETRIC LEAVES1 (AS1) and AS2 in leaf development in Arabidopsis thaliana: KNOX genes control five morphological events

The asymmetric leaves 1 ( as1 ) and as2 mutants of Arabidopsis thaliana exhibit pleiotropic phenotypes. Expression of a number of genes, including three class-1 KNOTTED -like homeobox ( KNOX ) genes ( BP , KNAT2 and KNAT6 ) and ETTIN / ARF3 , is enhanced in these mutants. In the present study, we attempted to identify the phenotypic features of as1 and as2 mutants that were generated by ectopic expression of KNOX genes, using multiple loss-of-function mutations of KNOX genes as well as as1 and as2 . Our results revealed that the ectopic expression of class-1 KNOX genes resulted in reductions in the sizes of leaves, reductions in the size of sepals and petals, the formation of a less prominent midvein, the repression of adventitious root formation and late flowering. Our results also revealed that the reduction in leaf size and late flowering were caused by the repression, by KNOX genes, of a gibberellin (GA) pathway in as1 and as2 plants. The formation of a less prominent midvein and the repression of adventitious root formation were not, however, related to the GA pathway. The asymmetric formation of leaf lobes, the lower complexity of higher-ordered veins, and the elevated frequency of adventitious shoot formation on leaves of as1 and as2 plants were not rescued by multiple mutations in KNOX genes. These features must, therefore, be controlled by other genes in which expression is enhanced in the as1 and as2 mutants.     

Biotechnological uses of cyanobacteria

Cyanobacteria (blue-green algae) are 0₂-evolving photosynthesizing prokaryotes that have an extensive history of use as a human food source and as a fertilizer in rice fields. They have also been recognized as an excellent source of vitamins and proteins and as such are found in health food stores in North America and elsewhere. Cyanobacteria have a great deal of potential as a source of fine chemicals, as a biofertilizer and as a source of renewable fuel. This potential is being realized as data from research in the areas of the physiology and chemistry of these organisms are gathered and as the knowledge of cyanobacterial genetics and genetic engineering increases. We review, here, the present (and possible future) uses of cyanobacteria and assess the state of the art with respect to the genetic manipulation of cyanobacteria.     

异构化的淀粉水解物用于短梗霉多糖发酵

短梗霉多糖; 发酵; 水解淀粉异构化;     

Variability in Race Tests with Heterodera glycines

Tests of Heterodera glycines on differential host plants to determine races were run in Arkansas, Illinois, and North Carolina to check the uniformity of results of the test. Methods used at the three locations varied somewhat. Results indicate that the race test is highly variable. Isolates previously identified as race 1 were identified as race 1 or race 3; those identified as race 2 were identified in these tests as race 2, 4, 9, or 14; those previously identified as race 3 were identified as race 1 or race 3; those identified as race 4 were identified in these tests as race 4 or race 14; those previously identified as race 5 were identified as race 2; and those previously identified as race 6 were identified as race 1, 2, 4, 5, or 6. Part of the variability resulted from the use of differential host plants from different sources and part from nonstandard differential host plants. Other variations may be due to inability to obtain completely uniform inoculum or to recover all nematodes that penetrated.     

Ethnobotany of Ghalegay,District Swat,Pakistan*

Ethnobotanical study of plants revealed that the local community of Ghalegy, District Swat, invariably uses 126 species of 59 families for various purposes. Based on their traditional local uses, fifty- seven species ( 4512%) were classified as medicinal, forty-seven as fire wood ( 3713%) , forty- five as forage ( 3517%) , twenty- eight as honey bee species ( 2212%) , twenty- seven as vegetable species ( 2114%) , 25 as edible fruits ( 14 wild and 11cultivated) , thirteen as timber wood ( 1013%) , twelve as ornamental ( 91 5%) , eleven as furniture wood, ten as shelter and thatch makers ( 719%) , ten as fencing ( 719%) , five as poisonous ( 4%) , four as religiousPsuperstitious species, three species used in making hand sticks and wooden tools ( 21 4%) , three as utensil cleaner species ( 214%) , three as evil repellent and one as fish poisoning species. The area is in plant resources and traditional knowledge but it needs ecological management for its sustainability.     

Rational design and characterization of bioplastics from Hermetia illucens prepupae proteins

In this study proteins extracted from prepupae of Hermetia illucens, also known as black soldier fly, are investigated as promising base for a new type of bioplastics for agricultural purposes. Design of experiments techniques are employed to perform a rational study on the effects of different combination of glycerol as plasticizer, citric acid as cross-linking agent and distilled water as solvent on the capability of proteins to form a free-standing film through casting technique, keeping as fixed the quantity of proteins. Glycerol shows interesting properties as plasticizer contributing to the formation of homogenous and free-standing film. Moreover, mechanical and thermal characterizations are performed to estimate the effect of increasing amounts of proteins on the final properties and thickness of the specimens. Proteins derived from H. illucens can be successfully employed as base for bioplastics to be employed for agricultural purposes.     

孕烷X受体的研究进展

核受体是一类高度保守的配体依赖性转录因子家族,在哺乳动物发育、繁殖、免疫应答、心血管功能、组织生长、肿瘤形成、外源物清除及糖类和脂质代谢等生理过程中发挥重要作用。机体对外源物质的清除主要是由孕烷X受体等核受雄介导的。孕烷X受体最早是作为外源物感受器而被研究的,可以被大多数亲脂性药物等外源性化合物及一些内源性化合物如胆汁酸等结构差异很大的配体激活,进而与视黄醇类X受体等形成异源二聚体,结合在ER6、XREM等DNA元件上,调控下游靶基因（包括一相代谢酶、二相结合酶及药物转运体等基因）的表达。此外,孕烷X受体在能量代谢和免疫反应中也有重要作用,参与某些代谢疾病的发生发展,且已在动物模型中被证明是Ⅱ型糖尿病、血脂异常、肥胖症和动脉粥样硬化等代谢疾病治疗的有效靶标。我们主要就其发现、结构、组织分布、作用方式、自身表达的调节等方面的最新研究进行综述。     

Biomarkers,natural variability,and risk assessment: Can they coexist?

This paper is a discussion of the utility of biomarkers as a component of the ecological risk assessment process. Both the pros and the cons of biomarkers are discussed, as well as consideration of some of the sources of variability. In the end, biomarkers are considered useful as long as we are aware of their limitations and sources of uncontrolled variability.     

Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties

Microbial fermentation is emerging as an increasingly important resource for the production of fatty acids to serve as precursors for renewable diesel as well as detergents, lubricants and other industrial chemicals, as an alternative to traditional sources of reduced carbon such as petroleum. A major disadvantage of fuels derived from biological sources is their undesirable physical properties such as high cloud and pour points, and high viscosity. Here we report the development of an Escherichia coli strain that efficiently produces anteiso-branched fatty acids, which can be converted into downstream products with lower cloud and pour points than the mixtures of compounds produced via the native metabolism of the cell. This work addresses a serious limitation that must be overcome in order to produce renewable biodiesel and oleochemicals that perform as well as their petroleum-based counterparts.     

Splenic lesions: FNA findings in 48 cases

OBJECTIVE: To study fine needle aspiration (FNA) cytological findings of splenic lesions and assess the role of FNA in the diagnosis of splenomegaly or splenic tumours. METHODS: This study consisted of 48 cases, 25 males and 23 females. The ages ranged between 3 and 71 years. Most of these cases were aspirated under ultrasonographic guidance and a small number were also aspirated directly by using a 22- to 23-gauge needles. The smears were stained with Wright-Giemsa and Papanicolaou methods. Special stains were used whenever necessary. RESULTS: In this study 14 cases were diagnosed as lymphoma-leukaemia, 7 cases as tuberculosis, 12 cases as kala-azar, 2 cases as hydatid cyst, 3 cases as storage diseases, 3 cases as simple cyst, 2 cases as myeloproliferative disorders, 2 cases as malignant tumours and 3 cases as hamartomas (these were wrongly diagnosed as malignant tumours). CONCLUSION: Splenic aspiration is a safe procedure and is very useful in the diagnosis of parasitic and infectious diseases, especially in endemic countries like Iran.     

SLX4: multitasking to maintain genome stability

The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF–ERCC1, MUS81–EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.     

Studies of oligoadenylate formation on a poly(U) template

We have studied a variety of condensation reactions involving poly (U) as template and isomeric adenosine dinucleotides as substrates. We find that [3'-5']-linked dinucleotides such as A3pA and pA3pA are better acceptors than the corresponding [2'-5']-linked compounds, while ImpA2pA is a better donor than ImpA3pA. The reaction between A2pA and ImpA3pA, for example, yields only 4% of product while the reaction of A3pA with ImpA2pA yields 86% of product. The more efficient condensation reactions of dimers are about as efficient as the self-condensation of ImpA. They yield a few percent of material in which five or more substrate molecules are linked together. The percentage of the natural [3'-5']-linkage in the product varies greatly, from as little as 1% to as much as 45%.     

What is Spanish nationalism today? From legitimacy crisis to unfulfilled renovation (1975–2000)

The article explores the different discourses on Spanish nationalism and 'patriotic affirmation' existing in contemporary Spain. Since the end of Francoism, Spanish nationalism has existed in a de-articulated and diffuse way, rather as a reaction against the challenge of stateless nationalisms than as a substantive doctrine. However, since the mid-1980s there has been a recovery of Spanish nationalist discourse, often labelled as 'Constitutional patriotism', whose main point is the insistence on History as the founding basis for the legitimation of the present Spanish polity, as well as the vindication of the 1978 Constitution as the end-point of decentralization.