Regular Simple Queues of Protein Contact Maps

A protein fold can be viewed as a self-avoiding walk in certain lattice model, and its contact map is a graph that represents the patterns of contacts in the fold. Goldman, Istrail, and Papadimitriou showed that a contact map in the 2D square lattice can be decomposed into at most two stacks and one queue. In the terminology of combinatorics, stacks and queues are noncrossing and nonnesting partitions, respectively. In this paper, we are concerned with 2-regular and 3-regular simple queues, for which the degree of each vertex is at most one and the arc lengths are at least 2 and 3, respectively. We show that 2-regular simple queues are in one-to-one correspondence with hill-free Motzkin paths, which have been enumerated by Barcucci, Pergola, Pinzani, and Rinaldi by using the Enumerating Combinatorial Objects method. We derive a recurrence relation for the generating function of Motzkin paths with \(k_i\) peaks at level i, which reduces to the generating function for hill-free Motzkin paths. Moreover, we show that 3-regular simple queues are in one-to-one correspondence with Motzkin paths avoiding certain patterns. Then we obtain a formula for the generating function of 3-regular simple queues. Asymptotic formulas for 2-regular and 3-regular simple queues are derived based on the generating functions.     

Bioactive effect of the preparation biostyl on the reproductive function of different genotypes of American mink

The different role of coat color mutations in the American mink on the per os effect of the biologically active preparation Biostyl was shown. The number of kits per female was the same in all control genotypes, including Standard (+/+ +/+), sapphire (a/a p/p), and lavender (a/a m/m): 4.4 ± 0.4, 4.4 ± 0.5, and 4.3 ± 0.5, respectively. Experimental groups of these genotypes have shown a great contrast among each other: stimulation of the reproductive function was 5.2 ± 0.3 in Standard minks, while suppression of the reproductive function was 3.8 ± 0.6, and 2.3 ± 0.5 in the double recessive mutants sapphire and lavender, respectively. The differentiation in body mass between experimental and control newborn Standard kits was not revealed. A significant decrease in the body mass of newborn experimental sapphire kits as compared to control group in a sex-specific manner was registered.     

The aromatic cytokinin <Emphasis Type="Italic">meta-</Emphasis>topolin promotes in vitro propagation,shoot quality and micrografting in <Emphasis Type="Italic">Corylus colurna</Emphasis> L.

The role of 4.1 or 8.2 μM meta-topolin (mT) on shoot multiplication, rooting and ex vitro acclimatization of micropropagated Corylus colurna L., a promising non-suckering rootstock for hazelnut (Corylus avellana L.), was examined in comparison to N⁶-benzyladenine (BA), the most used cytokinin in tissue culture of Corylus spp. The influence of 8.2 μM mT and BA on photosynthetic pigments content and antioxidant enzymes activity, catalase (CAT) and guaiacol peroxidase (POD), in regenerated shoots, and on the preparation of the rootstock for micrografting was also evaluated. The highest shoot multiplication was recorded on medium containing 8.2 μM mT and an overall positive effect of mT on growth and quality of micropropagated shoots was found. The highest chlorophyll a content (1.236 mg g^?1 fresh weight, FW) and chlorophyll a/b ratio (2.48), and the lowest total carotenoids content (0.292 mg g^?1 FW) and CAT activity (25.8 μmol min^?1 mg^?1 protein) were detected after 8.2 μM mT application, while no significant differences were found in chlorophyll b content and POD activity between the two cytokinins. The best rhizogenesis response (98% for 4.1 μM and 100% for 8.2 μM mT) and ex vitro acclimatization competence (higher than 78%) were exhibited from shoots multiplied on mT. Furthermore, the multiplication of rootstock on mT allowed obtaining the highest (70%) response of successful micrografting. The present findings provide the first evidence of the successful applicability of mT in C. colurna tissue culture and development of micrografted plantlets.     

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix

Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino acid substitution matrices to score amino acid pairs. The choice of substitution matrix strongly affects homology detection performance. We earlier proposed a substitution matrix named MIQS that was optimized for distant protein homology search. Herein we further evaluate MIQS in combination with LAST, a heuristic and fast database search tool with a tunable sensitivity parameter m, where larger m denotes higher sensitivity. Results show that MIQS substantially improves the homology detection and alignment quality performance of LAST across diverse m parameters. Against a protein database consisting of approximately 15 million sequences, LAST with m?=?10⁵ achieves better homology detection performance than BLASTP, and completes the search 20 times faster. Compared to the most sensitive existing methods being used today, CS-BLAST and SSEARCH, LAST with MIQS and m?=?10⁶ shows comparable homology detection performance at 2.0 and 3.9 times greater speed, respectively. Results demonstrate that MIQS-powered LAST is a time-efficient method for sensitive and accurate homology search.     

Impacts on Micro- and Macro-Structure of Thermally Stabilised Whey Protein-Pectin Complexes: A Fluorescence Approach

Stability of whey protein-pectin complexes is an essential criterion for their application in different food matrices. The impact of process parameters on micro- and macro-structural characteristics of thermally stabilised whey protein-pectin complexes was investigated using fluorescence spectroscopy, ζ-potential measurements, dynamic light scattering and phase separation. Complexes prepared from whey protein isolate (WPI) and pectins with different degrees of esterification (HMP, LMP) were generated at different biopolymer concentrations (WPI + pectin: 5.0 % + 1.0 %, c _{h i g h} ; 2.75 % + 0.55 %, c _{m e d} ; 0.5 % + 0.1 %, c _{l o w} ), heating temperatures (80-90^°C) and pH levels (6.1-4.0). Micro- and macro-structural characteristics of the complexes depended on concentration level and degree of esterification, with complexes being more sensitive towards environmental changes at c _{l o w} than at c _{m e d} and c _{h i g h} . WPI-LMP complexes exhibited sizes <1 μm suitable for micro-encapsulation, whereas WPI-HMP complexes at c _{m e d} achieved sizes from 1-10 μm and at c _{h i g h} from 10-200 μm underlining their potential as fat-replacers and structuring agents, respectively. Slopes and intercepts derived from intensity ratios of fluorescence spectra gave insights into the state of unfolding of β-lactoglobulin within the complexes and thus about the protective effect of pectin addition.     

Chaotic Dynamics of Neuromuscular System Parameters and the Problems of the Evolution of Complexity

The evolution rate v(t) varies among diverse biosystems, but a general theory can be formulated when the dynamics of the biosystem stater x = x(t) = (x₁, x₂, x _m ) ^T is considered in the m-dimensional space of states. A mathematical approach is proposed for evaluating such processes and describes the processes in terms of particular chaos of the statistical distribution functions f(x). In the case of complex multicomponent systems with a high dimension number m (m ?1) of the phase space of states, we propose using pairwise comparison matrices of samples x(t) when homeostasis is constant and calculating the parameters of quasiattractors. The Glensdorff–Prigogine thermodynamic approach to estimating evolution is inefficient in assessing the third-type systems, while it is applicable and the Prigogine theorem works at the level of molecular systems. Alterations in the state of the human neuromuscular system were found to lead to chaotic changes in the statistical functions f(x) in tremor recording samples, while quasiattractor parameters demonstrate a certain regularity.     

Change of Mendelian ratios and meiotic recombination parameters in F<Subscript>1</Subscript> hybrid tomatoes under the influence of γ-irradiation

The effect of γ-irradiation treatment of seeds of intra- and interspecific F₁ hybrid tomatoes on distortion of Mendelian monohybrid segregation, crossover variability, and recombination frequency of unlinked marker genes of chromosomes 2 and 6 was studied. It was found that more significant distortion effect on the segregation of marker loci of studied chromosomes was detected for seed treatment with 130 Gy. The significant direct relationship between Mendelian segregation for m-2 gene and a rf _m-2c vaue for 60 Gy and for aw and m-2 genes and rf _{aw c} , _{aw m-2} values for 60 and 130 Gy treatment in combination Mo500 × var. cerasiforme was revealed. The latter corresponds to the effect of “quasirepulsion.”     

Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring

Key message

An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring.

Abstract

Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4–63.0 % for spike length, 48.2–79.6 % for spikelet number per spike, 13.1–48.1 % for plant architecture, and 12.2–26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A ^m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.

     

Mesophyll conductance to CO<Subscript>2</Subscript> in leaves of Siebold’s beech (<Emphasis Type="Italic">Fagus crenata</Emphasis>) seedlings under elevated ozone

Ozone is an air pollutant that negatively affects photosynthesis in woody plants. Previous studies suggested that ozone-induced reduction in photosynthetic rates is mainly attributable to a decrease of maximum carboxylation rate (V_cmax) and/or maximum electron transport rate (J_max) estimated from response of net photosynthetic rate (A) to intercellular CO₂ concentration (C_i) (A/C_i curve) assuming that mesophyll conductance for CO₂ diffusion (g_m) is infinite. Although it is known that C_i-based V_cmax and J_max are potentially influenced by g_m, its contribution to ozone responses in C_i-based V_cmax and J_max is still unclear. In the present study, therefore, we analysed photosynthetic processes including g_m in leaves of Siebold’s beech (Fagus crenata) seedlings grown under three levels of ozone (charcoal-filtered air or ozone at 1.0- or 1.5-times ambient concentration) for two growing seasons in 2016–2017. Leaf gas exchange and chlorophyll fluorescence were simultaneously measured in July and September of the second growing season. We determined the A, stomatal conductance to water vapor and g_m, and analysed A/C_i curve and A/C_c curve (C_c: chloroplast CO₂ concentration). We also determined the Rubisco and chlorophyll contents in leaves. In September, ozone significantly decreased C_i-based V_cmax. At the same time, ozone decreased g_m, whereas there was no significant effect of ozone on C_c-based V_cmax or the contents of Rubisco and chlorophyll in leaves. These results suggest that ozone-induced reduction in C_i-based V_cmax is a result of the decrease in g_m rather than in carboxylation capacity. The decrease in g_m by elevated ozone was offset by an increase in C_i, and C_c did not differ depending on ozone treatment. Since C_c-based V_cmax was also similar, A was not changed by elevated ozone. We conclude that g_m is an important factor for reduction in C_i-based V_cmax of Siebold’s beech under elevated ozone.     

Evolution of protein transport to the chloroplast envelope membranes

Comparing with other angiosperms, most members within the family Orchidaceae have lower photosynthetic capacities. However, the underlying mechanisms remain unclear. Cypripedium and Paphiopedilum are closely related phylogenetically in Orchidaceae, but their photosynthetic performances are different. We explored the roles of internal anatomy and diffusional conductance in determining photosynthesis in three Cypripedium and three Paphiopedilum species, and quantitatively analyzed their diffusional and biochemical limitations to photosynthesis. Paphiopedilum species showed lower light-saturated photosynthetic rate (A _N), stomatal conductance (g _s), and mesophyll conductance (g _m) than Cypripedium species. A _N was positively correlated with g _s and g _m. And yet, in both species A _N was more strongly limited by g _m than by biochemical factors or g _s. The greater g _s of Cypripedium was mainly affected by larger stomatal apparatus area and smaller pore depth, while the less g _m of Paphiopedilum was determined by the reduced surface area of mesophyll cells and chloroplasts exposed to intercellular airspace per unit of leaf area, and much thicker cell wall thickness. These results suggest that leaf anatomical structure is the key factor affecting g _m, which is largely responsible for the difference in photosynthetic capacity between those two genera. Our findings provide new insight into the photosynthetic physiology and functional diversification of orchids.     

High-density linkage maps for <Emphasis Type="Italic">Citrus sunki</Emphasis> and <Emphasis Type="Italic">Poncirus trifoliata</Emphasis> using DArTseq markers

The construction of a high-resolution genetic map of citrus would be of great value to breeders and to associate genomic regions with characteristics of agronomic interest. Here, we describe a novel high-resolution map of citrus using a population derived from a controlled cross between Citrus sunki (female parent) and Poncirus trifoliata (male parent). The genetic linkage maps were constructed using DArTseq markers and a pseudo-testcross strategy; only markers showing the expected segregation ratio were considered. To investigate synteny, all markers from both linkage maps were aligned with the genome of Citrus sinensis. The C. sunki map has a total of 2778 molecular markers and a size of 2446.6 cM, distributed across ten linkage groups. The map of P. trifoliata was built with 3084 markers distributed in a total of nine linkage groups, with a total size of 2411.6 cM. These maps are the most saturated linkage maps available for C. sunki and P. trifoliata and have high genomic coverage. We also demonstrated that the maps reported here are closely related to the reference genome of C. sinensis.     

Heterologous expression of an RNA-binding protein affects flowering time as well as other developmental processes in <Emphasis Type="Italic">Solanaceae</Emphasis>

Flowering time in members of the Solanaceae plant family, such as pepper (Capsicum spp.) and tomato (Solanum lycopersicum), is an important agronomic trait for controlling shoot architecture and improving yield. To investigate the feasibility of flowering time regulation in tomato, an RNA-binding protein (RBP) encoding gene homologous to human Nucleolar protein interacting with the forkhead-associated (FHA) domain of pKI-67 (NIFK), CaRBP, was isolated from hot pepper. The function of CaRBP was determined in transgenic tomato. The deduced amino acid sequence includes an RNA recognition motif (RRM) and showed most similarity to the RRM present in a putative RBP encoded by human NIFK. CaRBP was highly expressed in the vegetative and reproductive tissues, such as leaves and fruits, respectively. Subcellular localization analysis indicated that CaRBP is a nucleolar protein. Heterologous expression of CaRBP under 35S promoter in tomato plants induced severe alteration of flowering with additional defects of vegetative organs. This floral retardation was associated with the alteration of SFT/SP3D and SlSOC1s as floral integrators. Furthermore, CaRBP reduces the expression levels of SlCOLs/TCOLs via changes in the expression of SlCDF3, SlFBHs, and SlFKF1s. This indicates a repressive effect of CaRBP on the regulation of flowering time in tomato. Overall, these results suggest that alteration in CaRBP expression levels may provide an effective means of controlling flowering time in day-neutral Solanaceae.     

Mapping and characterization of wheat stem rust resistance genes <Emphasis Type="Italic">SrTm5</Emphasis> and <Emphasis Type="Italic">Sr60</Emphasis> from <Emphasis Type="Italic">Triticum monococcum</Emphasis>

Key message

The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5A^mS, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22.

Abstract

The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7A^mL, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5A^mS that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC–NBS–LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60.

     

Molecular characterization of <Emphasis Type="Italic">bmyC</Emphasis> gene of the mosquito pupicidal bacteria, <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> (VCRC B483) and in silico analysis of bacillomycin D synthetase C protein

A strain of Bacillus amyloliquefaciens (VCRC B483) exhibiting mosquito pupicidal, keratinase and antimicrobial activities was isolated from mangrove forest ecosystem of Andaman and Nicobar Islands. Molecular characterization of the strain showed the presence of lipopeptide encoding bmyC gene. Phylogenetic tree based on protein sequence of this gene exhibited homology with mycosubtilin synthetase of Bacilus atropheus and Iturin synthetase of Bacillus subtilis and B. amyloliquefaciens. This is the first report on the evolutionary conservation of amino acids concerned with the function and structure of bmyC protein of B. amyloliquefaciens. The presence of valine at the 1197th position in our strain was found to be unique and different from the existing strains of B. subtilis and B. amyloliquefaciens. Molecular modelling studies revealed significant changes in the structure of epimerization domain of the bmyC protein with A1197V variation. Crude metabolite of this strain exhibited antifungal activity against Fusarium sp. and Carvularia sp.     

In Vitro Functional Characterisation of Cytochrome P450 (CYP) 2C19 Allelic Variants <Emphasis Type="Italic">CYP2C19*23</Emphasis> and <Emphasis Type="Italic">CYP2C19*24</Emphasis>

Cytochrome P450 (CYP) 2C19 is essential for the metabolism of clinically used drugs including omeprazole, proguanil, and S-mephenytoin. This hepatic enzyme exhibits genetic polymorphism with inter-individual variability in catalytic activity. This study aimed to characterise the functional consequences of CYP2C19*23 (271 G>C, 991 A>G) and CYP2C19*24 (991 A>G, 1004 G>A) in vitro. Mutations in CYP2C19 cDNA were introduced by site-directed mutagenesis, and the CYP2C19 wild type (WT) as well as variants proteins were subsequently expressed using Escherichia coli cells. Catalytic activities of CYP2C19 WT and those of variants were determined by high performance liquid chromatography-based essay employing S-mephenytoin and omeprazole as probe substrates. Results showed that the level of S-mephenytoin 4′-hydroxylation activity of CYP2C19*23 (V _max 111.5 ± 16.0 pmol/min/mg, K _m 158.3 ± 88.0 μM) protein relative to CYP2C19 WT (V _max 101.6 + 12.4 pmol/min/mg, K _m 123.0 ± 19.2 μM) protein had no significant difference. In contrast, the K _m of CYP2C19*24 (270.1 ± 57.2 μM) increased significantly as compared to CYP2C19 WT (123.0 ± 19.2 μM) and V _max of CYP2C19*24 (23.6 ± 2.6 pmol/min/mg) protein was significantly lower than that of the WT protein (101.6 ± 12.4 pmol/min/mg). In vitro intrinsic clearance (CL_int = V _max/K _m) for CYP2C19*23 protein was 85.4 % of that of CYP2C19 WT protein. The corresponding CL_int value for CYP2C19*24 protein reduced to 11.0 % of that of WT protein. These findings suggested that catalytic activity of CYP2C19 was not affected by the corresponding amino acid substitutions in CYP2C19*23 protein; and the reverse was true for CYP2C19*24 protein. When omeprazole was employed as the substrate, K _m of CYP2C19*23 (1911 ± 244.73 μM) was at least 100 times higher than that of CYP2C19 WT (18.37 ± 1.64 μM) and V _max of CYP2C19*23 (3.87 ± 0.74 pmol/min/mg) dropped to 13.4 % of the CYP2C19 WT (28.84 ± 0.61 pmol/min/mg) level. Derived from V _max/K _m, the CL_int value of CYP2C19 WT was 785 folds of CYP2C19*23. K _m and V _max values could not be determined for CYP2C19*24 due to its low catalytic activity towards omeprazole 5′-hydroxylation. Therefore, both CYP2C19*23 and CYP2C19*24 showed marked reduced activities of metabolising omeprazole to 5-hydroxyomeprazole. Hence, carriers of CYP2C19*23 and CYP2C19*24 allele are potentially poor metabolisers of CYP2C19-mediated substrates.     

The involvement of TsFtsH8 in <Emphasis Type="Italic">Thellungiella salsuginea</Emphasis> tolerance to cold and high light stresses

Thellungiella salsuginea is a plant that commonly grows in harsh environments of salinity and low temperature. Although the molecular mechanism underlying salt tolerance in T. salsuginea has been extensively explored, our understanding of how this species tolerates cold stress is limited. In a previous study, Wong et al. (2006) identified a cold-inducible TsFtsH8 gene in T. salsuginea. Based on the role of AtFtsH in D1 protein turnover and in maintaining the normal function of photosystem II, we hypothesized that TsFtsH8 might be related to cold tolerance in T. salsuginea. In the present study, RNAi lines of TsFtsH8 were generated and its tolerance to cold was evaluated. The results showed that in early spring, TsFtsH8-RNAi lines underwent leaf variegation, severe chlorophyll decomposition, organelle deterioration, decrease in the maximum photochemical efficiency of photosystem II (F _v /F _m) and in the proportion of open photosystem II reaction centers (qP), and incomplete degradation of the 23 kDa fragment of the D1 protein. These findings suggest that TsFtsH8 is involved in the development of T. salsuginea in the early spring.     

Enzymological properties of endo-(1–4)-β-glucanase Eg12p of <Emphasis Type="Italic">Penicillium canescens</Emphasis> and characteristics of structural gene <Emphasis Type="Italic">egl2</Emphasis>

Gene egl2 of secreted endo-(1–4)-β-glucanase of glycosyl hydrolase family 5 of the mycelial fungus Penicillium canescens was cloned. The gene was expressed in P. canescens under control of a strong promoter of the bgaS gene encoding β-galactosidase of P. canescens, and endoglucanase producing strains were obtained. Chromatographically purified recombinant 48 kDa protein had pH and temperature optima 3.4 and 60°C, respectively, exhibited specific activity of 33 IU, and had K _m and V _max in CM-cellulose hydrolysis of 10.28 g/liter and 0.26 μmol/sec per mg, respectively.     

Intrapopulation heterogeneity of the fluorescence parameters of the marine plankton alga <Emphasis Type="Italic">Thalassiosira weissflogii</Emphasis> at various nitrogen levels

Fluorescence of the marine alga Thalassiosira weissflogii (Grunow) Fryxell et Hasle with open (F _o ) and closed (F _m ) reaction centers of photosystem 2 (PS 2) and its relative variable fluorescence (F _v/F _m ) were measured at various levels of inorganic nitrogen. A significant heterogeneity of the population in terms of these parameters was revealed. Some cells within the population were more sensitive to nitrogen deficiency, and their photosynthetic apparatus was disrupted to a greater extent. The cells within a population also differed in terms of their ability to recover after incubation at low nitrogen levels. Enhancement of nitrogen deficiency resulted in an increase in the variability of the F _o and F _v/F _m values of the cells. Fluorescence variability decreased at a less pronounced deficiency. Fluorescence variability should be taken into consideration in the studies concerning responses of algae to changes in nutrient contents.