Handling class imbalance problem in miRNA dataset associated with cancer

MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3'' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5'' UTR and Coding sequences (CDS). Complementarity binding of miRNA to mRNA target sites either results in complete degradation of the mRNA itself or it may regulate the mRNA as an oncogene or as a tumor suppressor gene. However, the exact mechanism involved in identifying a miRNA to be associated with cancer is still unclear. Further, with the outburst in the number of miRNAs sequences recorded every year in miRBase, the gap is still widening mainly due to the laborious and economically unfavorable experimental procedures associated with the functional annotation. Motivated by the fact, we constructed a two-step support vector machine-based predictive model - miRSEQ and miRINT. However, the major pitfall during the construction of the model is the class imbalance problem. Hence, in order to overcome class imbalance problem, in the present study we empirically compare the effectiveness of two different methods viz., Synthetic Minority Oversampling Technique (SMOTE) and cost-senstive learning method. Performance measures were evaluated in terms of Precision and Recall. Based on our result, it was observed that for miRNA dataset with high class imbalance utilized for predicting association of cancer, cost-sensitive method outperformed the oversampling method.     

Attachment styles impact on pet visitation effectiveness

Abstract

This paper describes a field study on the effects of attachment styles on the subjective well-being of institutionalized older persons after participating in a pet visitation program. We compared how attachment style (i.e., secure, anxious ambivalent, dismissive avoidant, and fearful avoidant) moderated the impact of a dog visitation program in 52 elderly residents of an assisted-living facility. Controlling for pre-visitation mood, the results revealed that the secure style related to increases in positive mood after interacting with the dogs. The anxious ambivalent style related to increases in positive mood and decreases in ratings of depression. Most importantly, the fearful avoidant style related to increases in depression after interacting with the dogs. The results highlight the notion that not all participants benefit from taking part in pet visitation programs. Theoretically, this study presents preliminary evidence for the relevance of attachment styles in understanding human–pet interactions.     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

Conditional lethality involving a cytoplasmic mutant and chlorophyll-deficient malate dehydrogenase mutants in soybean

Summary Conditional lethality in soybean, Glycine max (L.) Merr., occurred in F₂ plants when cytoplasmicchlorophyll mutant Genetic Type T275 was the female parent and when either nuclear mutants T253 or T323 plants were the male parents. Mutant T253 [Mdh1-n (Urbana) y20 (Urbana) k2] is missing two of three mitochondrial malate dehydrogenase isozymes [Mdh1-n (Urbana)] and has yellowish-green leaves [y20 (Urbana)] and a tan-saddle pattern seed coat (k2). Mutant T323 [Mdh1-n (Ames 2) y20 (Ames 2)] also is missing two of three mitochondrial malate dehydrogenase isozymes [Mdh1-n (Ames 2)] and has yellowishgreen leaves [y20 (Ames 2)], but has yellow seed coat (K2). Mutants T275, T253, and T323 are viable both in the field and glasshouse. The genotypes cyt-Y2 Mdh1-n (Urbana) y20 (Urbana) k2/Mdh1-n (Urbana) y20 (Urbana) k2 and cyt-Y2 Mdh1-n (Ames 2) y20 (Ames 2)/Mdh1-n (Ames 2) y20 (Ames 2) are conditional lethals. These genotypes are lethal under field conditions, but plants survive in reduced light under shadecloth in the glasshouse. We do not know if their interaction with cyt-Y2 is due to Mdh1-n, y20, or Mdh1-n y20. The reciprocal cross (cyt-Y2 as male parent) gives viable genotypes. These conditional lethal genotypes should be useful for studies on the interaction between organelle and nuclear genomes.This is journal paper no. J-14777 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011-1010. Project 2985     

Synthesis and Analysis of Nucleosides Bearing Pyrrolepolyamide Binding to DNA

Abstract

An efficient synthesis of adenosine bearing pyrrolepolyamide 1 was achieved by coupling of 3 with 2. The CD spectra obtained at several [ligand ]/[duplex] ratios allowed verification of the formation complex of the DNA duplex [d(CGCAAATTGGC)/d(GCCAATTTGCG)] with 1.     

陕西省新型城镇化与生态环境协调度研究

城镇化与生态环境之间相互影响、相互促进，两系统间耦合协调状态对于区域绿色可持续发展意义重大。以陕西省2005—2019年数据为例，在构建新型城镇化与生态环境系统评价指标体系的基础上结合耦合协调度模型、相对发展模型及面板向量自回归(PVAR)模型分析新型城镇化系统与生态环境系统间的耦合协调时空规律及互动关系。结果表明：(1)陕西省耦合协调度总体呈现“基本不协调—基本协调—中度协调”的演变规律。(2)各市耦合协调发展状态空间差异明显，2005年、2013年、2019年陕西省10个城市新型城镇化与生态环境耦合协调发展状态存在较大差异性，相对发展状态整体上由新型城镇化滞后状态发展为生态环境滞后状态。(3)脉冲响应图反映出新型城镇化与生态环境两系统间存在明显互动关系，前期生态环境受新型城镇化冲击的负向抑制作用，后期影响逐渐减小，受自身冲击较大，而新型城镇化发展前后期均主要受自身影响。本研究认为新型城镇化发展必须以生态为优先，在提高生态承载力的基础上，加速提升陕西省各区域空间人口等不同维度城镇化发展水平，从而实现高质量可持续的绿色发展目标。     

Essential role of MESP1-RING1A complex in cardiac differentiation

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Constructing more informative plant–pollinator networks: visitation and pollen deposition networks in a heathland plant community

Interaction networks are widely used as tools to understand plant–pollinator communities, and to examine potential threats to plant diversity and food security if the ecosystem service provided by pollinating animals declines. However, most networks to date are based on recording visits to flowers, rather than recording clearly defined effective pollination events. Here we provide the first networks that explicitly incorporate measures of pollinator effectiveness (PE) from pollen deposition on stigmas per visit, and pollinator importance (PI) as the product of PE and visit frequency. These more informative networks, here produced for a low diversity heathland habitat, reveal that plant–pollinator interactions are more specialized than shown in most previous studies. At the studied site, the specialization index was lower for the visitation network than the PE network, which was in turn lower than for the PI network. Our study shows that collecting PE data is feasible for community-level studies in low diversity communities and that including information about PE can change the structure of interaction networks. This could have important consequences for our understanding of threats to pollination systems.     

Phospholipid dependence of the anion transport system of the human erythrocyte membrane. Studies on reconstituted band 3/lipid vesicles

Band 3 protein extracted from human erythrocyte membranes by Triton X-100 was recombined with the major classes of phospholipid occurring in the erythrocyte membrane. The resulting vesicle systems were characterized with respect to recoveries, phospholipid composition, protein content and vesicle size as well as capacity and activation energy of sulfate transport. Transport was classified into band-3-specific fluxes and unspecific permeability by inhibitors. Transport numbers (sulfate ions per band 3 per minute) served as a measure of functional recovery after reconstitution. The transport properties of band 3 proved to be insensitive to replacement of phosphatidylcholine by phosphatidylethanolamine, while sphingomyelin and phosphatidylserine gradually inactivated band-3-specific anion transport when present at mole fractions exceeding 30 mol%. The activation energy of transport remained unaltered in spite of the decrease in transport numbers. The results, which are discussed in terms of requirements of band 3 protein function with respect to the fluidity and surface charge of its lipid environment, provide a new piece of evidence that the transport function of band 3 protein depends on the properties of its lipid environment just as the catalytic properties of some other membrane enzymes. The well-established species differences in anion transport (Gruber, W. and Deuticke, B. (1973) J. Membrane Biol. 13, 19–36) may to some extent reflect this lipid dependence.