Flavonoid pattern and systematics of the genus Leucocyclus

The flavonoid pattern of the monotypic Turkish genus Leucocyclus consists of C-glycosylflavones (isovitexin; isoorientin and derivatives; several di-C-glycosylapigenins; schaftoside, isoschaftoside and vicenin-3; lucenin-2), of flavonol 3-O-glycosides (quercetin and kaempferol 3-O-rhamnoglucoside) and trace amounts of luteolin 7-O-rhamnoglucoside. The systematic significance of the flavonoid diversification within Leucocyclus as well as possible relationships to other genera of the Anthemideae are discussed.     

固定化葡萄糖异构酶最适pH值的调节

用多孔强碱性三乙醇胺基聚苯乙烯树脂作为载体,用CNBr与载体上多羟基作用共价偶联葡萄糖异构酶(GI)。最适偶联条件表明:CNBr量增多,蛋白载量增加,但比活下降。固定化葡萄糖异构酶(IGI)最适反应温度比天然酶提高15℃。并系统地研究了影响IGI活力-pH的曲线的各种因素:用具有不同平均孔径的载体(R=137A,185A,230A,365A)固定化GI,在低离子强度条件下(0.0064mol/L),测定其最适pH值分别7.76,7.56,7.50,8.20。选择平均孔径为230A且具有不同数量三乙醇胺基的载体(0.94,1.05,1.13,1.37mmol/g干胶)分别固定化GI,其最适pH值分别为7.70,7.50,7.46,7.36。     

Determination of total and active immobilized enzyme distribution in porous solid supports

The total and active immobilized enzyme (IME) distributions in porous supports are studied both theoretically and experimentally. In order to determine experimentally the enzyme distribution profiles within a single particle, we construct a diffusion cell containing controlled-pore glass particles such that the cell would mimic a large pellet support. Our purpose is to study the interplay between the diffusion process within the interparticle void space and immobilization process in the controlled-pore glass particles onto the evolution of the (total and active) enzyme distributions. A mathematical model is developed to describe the interaction of various processes within the diffusion cell. The immobilized enzymes are determined for a system of trypsin and controlled-pore glass particles. The total amount of enzymes are determined by the amino acid analysis, and the active fraction is obtained by an active-site titration. The experimentally measured total IME profiles compare very well with that predicted by the model. The determined active enzyme profile is found to be nonuniform one, and it represents about 40% of the total enzyme immobilized in the support particles.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Canopy structure,nitrogen distribution and whole canopy photosynthetic carbon gain in growing and flowering stands of tall herbs

Using a combination of mathematical modeling and field studies we showed that in dense stands of growing herbaceous plants the vertical pattern of leaf nitrogen distribution resembles the pattern of mean light attenuation in the stand and hence tends to maximize total daily photosynthetic carbon gain of the whole stand. Flowering represents a strong sink of nitrogen away from the photosynthetic apparatus and in herbs like Solidago altissima it induces leaf shedding. We studied both the effect of nitrogen reallocation and leaf shedding on the whole canopy photosynthesis and changes in leaf nitrogen distributions in stands moving from the growing to the flowering stage. Despite a decrease in leaf area index and total nitrogen available for photosynthesis in the flowering stand, the leaf nitrogen distribution here also leads to an almost maximum canopy photosynthesis. In both the growing and the flowering stands the leaf area index was higher than calculated optimum values. It is pointed out that this should not necessarily be interpreted as non-adaptive.     

DNA polymerase activity in developmental stages of Drosophila melanogaster

An assay procedure was developed that allowed the first reproducible measurement of DNA polymerase activity in all developmental stages of Drosophila melanogaster. Evidence is presented that the same enzymatic species is present in extracts of embryos, pupae, and adults of both sexes and that this activity has many properties similar to vertebrate α-polymerases. Polymerase activity per individual is low in embryos and rises steadily through larval instars, reaches a peak in early pupae, declines through the late pupal period, and remains low in newly eclosed adults of both sexes. A dramatic increase is observed in adult females as mature oocytes are formed. This pattern of enzyme activity is completely coincident with changes in DNA levels during development, and suggests that the Drosophila enzyme, like vertebrate α-polymerases, functions in cellular DNA replication. Two mutagen-sensitive mutants, deficient in both replication on undamaged templates and postreplication repair, were found to have normal levels of this α-polymerase activity. Our results suggest that a single enzymatic species of α-polymerase holoenzyme exists in Drosophila and is common to all developmental stages of this organism.     

Periodic Forces Trigger a Complex Mechanical Response in Ubiquitin

Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.     

LNRLMI: Linear neighbour representation for predicting lncRNA‐miRNA interactions

LncRNA and miRNA are key molecules in mechanism of competing endogenous RNAs(ceRNA), and their interactions have been discovered with important roles in gene regulation. As supplementary to the identification of lncRNA‐miRNA interactions from CLIP‐seq experiments, in silico prediction can select the most potential candidates for experimental validation. Although developing computational tool for predicting lncRNA‐miRNA interaction is of great importance for deciphering the ceRNA mechanism, little effort has been made towards this direction. In this paper, we propose an approach based on linear neighbour representation to predict lncRNA‐miRNA interactions (LNRLMI). Specifically, we first constructed a bipartite network by combining the known interaction network and similarities based on expression profiles of lncRNAs and miRNAs. Based on such a data integration, linear neighbour representation method was introduced to construct a prediction model. To evaluate the prediction performance of the proposed model, k‐fold cross validations were implemented. As a result, LNRLMI yielded the average AUCs of 0.8475 ± 0.0032, 0.8960 ± 0.0015 and 0.9069 ± 0.0014 on 2‐fold, 5‐fold and 10‐fold cross validation, respectively. A series of comparison experiments with other methods were also conducted, and the results showed that our method was feasible and effective to predict lncRNA‐miRNA interactions via a combination of different types of useful side information. It is anticipated that LNRLMI could be a useful tool for predicting non‐coding RNA regulation network that lncRNA and miRNA are involved in.