Tree Shape Research Articles

Preparation, Characterization, and In Vitro Evaluation of the Biological Activity of Several Metal-Based Complexes with Two Widely Used Fluoroquinolone Antibiotics: Lomefloxacin and Pefloxacin Drugs

Lomefloxacin (F1) and pefloxacin (F2) have a broad spectrum of antimicrobial activities against gram-positive and gram-negative bacteria. In this study, we investigated the complexation mode, morphological, and biological properties of four metal-based complexes of F1 and F2 molecules with Mg(II), Ca(II), Zn(II), and Fe(III) metal ions. These complexes were prepared at ~60–70 °C in a neutral medium using a 5% NH3 solution at ph ~7–8 with a 1:1 ratio. Multiple physicochemical methods were employed to characterize the binding mode between F1 and F2 with the metal ions under investigation. The results of these methods suggested that the gross formula of the complexes obtained with the metal ions were [mgf1(H2O)Cl]⋅2H2O, [caf1(H2O)Cl]⋅3H2O, [znf1(H2O)Cl], [fef1(H2O)2Cl2]⋅Cl⋅2H2O, [mgf2(H2O)Cl]⋅2H2O, [caf2(H2O)Cl]⋅3H2O, [znf2(H2O)Cl], and [fef2(H2O)2Cl2]⋅Cl⋅2H2O. The microscopic characterizations indicated that the Ca(II)-F1 complex had an interesting surface topography. Its particles had a homogenous, short, rod-like shaped structure that clustered together to form a tree shape. Using the Kirby–Bauer disc diffusion protocol, the synthesized metal-based complexes were screened in vitro against different gram-positive and gram-negative bacterial and fungal species. The antimicrobial profile of the Fe(III)-F1 complex indicated that it had remarkable inhibitory activity against all the tested bacterial and fungal species with a potency equal to that of the standard drugs (streptomycin and ketoconazole).

A Study of the Molecular Regulatory Network of VcTCP18 during Blueberry Bud Dormancy.

BRANCHED1 (BRC1) is a crucial member of the TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) gene family and is well known for playing a central role in shoot branching by controlling buds' paradormancy. However, the expression characteristics and molecular regulatory mechanism of BRC1 during blueberry bud dormancy are unclear. To shed light on these topics, shoots of three blueberry cultivars with different chilling requirements (CRs) were decapitated in summer to induce paradormancy release and subjected to different levels of chilling in winter to induce endodormancy release. The results showed that the high-CR cultivar 'Chandler' had the strongest apical dominance among the three cultivars; additionally, the expression of VcTCP18, which is homologous to BRC1, was the highest under both the decapitation treatment and low-temperature treatment. The 'Emerald' cultivar, with a low CR, demonstrated the opposite trend. These findings suggest that VcTCP18 plays a negative regulatory role in bud break and that there may be a correlation between the CR and tree shape. Through yeast 1-hybrid (Y1H) assays, we finally screened 21 upstream regulatory genes, including eight transcription factors: zinc-finger homeodomain protein 1/4/5/9, MYB4, AP2-like ethylene-responsive transcription factor AINTEGUMENTA (ANT), ASIL2-like, and bHLH035. It was found that these upstream regulatory genes positively or negatively regulated the expression of VcTCP18 based on the transcriptome expression profile. In summary, this study enriched our understanding of the regulatory network of BRCl during bud dormancy and provided new insights into the function of BRC1.

Spaces of Phylogenetic Diversity Indices: Combinatorial and Geometric Properties

Biodiversity is a concept most naturally quantified and measured across sets of species. However, for some applications, such as prioritising species for conservation efforts, a species-by-species approach is desirable. Phylogenetic diversity indices are functions that apportion the total biodiversity value of a set of species across its constituent members. As such, they aim to measure each species’ individual contribution to, and embodiment of, the diversity present in that set. However, no clear definition exists that encompasses the diversity indices in current use. This paper presents conditions that define diversity indices arising from the phylogenetic diversity measure on rooted phylogenetic trees. In this context, the diversity index ‘score’ given to a species represents a measure of its unique and shared evolutionary history as displayed in the underlying phylogenetic tree. Our definition generalises the diversity index notion beyond the popular Fair Proportion and Equal-Splits indices. These particular indices may now be seen as two points in a convex space of possible diversity indices, for which the boundary conditions are determined by the underlying shape of each phylogenetic tree. We calculated the dimension of the convex space associated with each tree shape and described the extremal points.

Seeing the Forest for the Trees: Mapping Cover and Counting Trees from Aerial Images of a Mangrove Forest Using Artificial Intelligence

Mangrove forests provide valuable ecosystem services to coastal communities across tropical and subtropical regions. Current anthropogenic stressors threaten these ecosystems and urge researchers to create improved monitoring methods for better environmental management. Recent efforts that have focused on automatically quantifying the above-ground biomass using image analysis have found some success on high resolution imagery of mangrove forests that have sparse vegetation. In this study, we focus on stands of mangrove forests with dense vegetation consisting of the endemic Pelliciera rhizophorae and the more widespread Rhizophora mangle mangrove species located in the remote Utría National Park in the Colombian Pacific coast. Our developed workflow used consumer-grade Unoccupied Aerial System (UAS) imagery of the mangrove forests, from which large orthophoto mosaics and digital surface models are built. We apply convolutional neural networks (CNNs) for instance segmentation to accurately delineate (33% instance average precision) individual tree canopies for the Pelliciera rhizophorae species. We also apply CNNs for semantic segmentation to accurately identify (97% precision and 87% recall) the area coverage of the Rhizophora mangle mangrove tree species as well as the area coverage of surrounding mud and water land-cover classes. We provide a novel algorithm for merging predicted instance segmentation tiles of trees to recover tree shapes and sizes in overlapping border regions of tiles. Using the automatically segmented ground areas we interpolate their height from the digital surface model to generate a digital elevation model, significantly reducing the effort for ground pixel selection. Finally, we calculate a canopy height model from the digital surface and elevation models and combine it with the inventory of Pelliciera rhizophorae trees to derive the height of each individual mangrove tree. The resulting inventory of a mangrove forest, with individual P. rhizophorae tree height information, as well as crown shape and size descriptions, enables the use of allometric equations to calculate important monitoring metrics, such as above-ground biomass and carbon stocks.

Study on the Phenotypic Diversity of 33 Ornamental Xanthoceras sorbifolium Cultivars

Xanthoceras sorbifolium, belonging to the family Sapindaceae, has a beautiful tree shape, elegant leaves, large and many brightly colored flowers, and a long flowering duration. This plant is widely applied in gardens. In this study, 33 cultivars of Xanthoceras sorbifolium were selected from the perspective of ornamental properties, and their phenotypic traits, such as leaves, flowers, and branches, were measured and analyzed, and their phenotypic diversity was comprehensively evaluated using principal component analysis, in order to investigate the phenotypic diversity characteristics of Xanthoceras sorbifolium. The results showed that the genetic diversity index of the qualitative traits varied from 0.14 to 1.50, and that of quantitative traits varied from 1.76 to 2.05. The quantitative traits were more diverse than the qualitative traits. The coefficient of variation of the qualitative traits ranged from 16.90% to 57.96%, and that of quantitative traits ranged from 12.92% to 32.87%. The phenotypic traits of the tested cultivars had relatively rich variation. Furthermore, the level of the phenotypic diversity index of Xanthoceras sorbifolium was not consistent with the level of coefficient of variation, indicating large variation and uneven distribution of variation. Through principal component analysis, 17 quantitative characters were extracted into five principal components, with a cumulative contribution rate of 79.82%, representing the primary information on the quantitative characters of ornamental Xanthoceras sorbifolium cultivars. The F value of the 33 samples ranged from –2.79 to 1.93, and the comprehensive scores of seven cultivars were greater than 1, indicating that these cultivars had rich phenotypic diversity. Therefore, the screening, development, and utilization of fine germplasm resources of Xanthoceras sorbifolium should focus on these cultivars. The 33 cultivars were subsequently clustered into five categories through systematic clustering. The cluster analysis provided references for breeding ornamental Xanthoceras sorbifolium cultivars with different utilization values, such as large white flowers, small red flowers, large red flowers, large orange flowers, and double-petaled flowers.

DEVELOPING A TECHNOLOGY FOR PRODUCING DRONE-BORNE HYPERSPECTRAL IMAGES TO MONITOR LARGE-AREA MIXED HERITAGE

Abstract. This study compared differences in the shooting and pre-processing techniques between manned and unmanned aerial images, and verified the precision of the images by comparing the ground sample distance between them. GSD of manned aerial image taken at high altitude could not discern tree shapes from 150 cm per pixel, but unmanned aerial image taken at low altitude (200 m) could distinguish trees individually with 30 cm per pixel. It, therefore, found that it is efficient and economically effective to produce unmanned hyperspectral images within the large-area mixed heritage. In addition, the unmanned aerial images have lower atmospheric errors and the ground sample distance that is high enough to distinguish individual trees, so they were found to be applied to the monitoring and the diagnosis for understanding the vegetation management and the health of the large-area mixed heritage.

Effect of Low-Light Stress on Sugar and Acid Accumulation during Fruit Development and Ripening of Sweet Cherry

In the production process of sweet cherry, there are unreasonable planting densities and tree shape selections. With increasing tree age, the crown of the tree continues to expand and the tree body is prone to canopy closure, which leads to the inability to efficiently use space and light energy. Low-light has become a major limiting factor in the quality of sweet cherry. Therefore, we analyzed the changes of various physiological indicators and the transcriptome of ‘Hongdeng’ sweet cherry under shading treatment in this study to investigate the effects of low-light stress on the photosynthetic characteristics of sweet cherry leaves and fruit physiology and biochemistry. The results showed that shading significantly reduces the light capture capacity of leaves, damages the photosystem, reduces carbon assimilation capacity, and consumes the majority of the captured light energy as photochemical energy, thereby restricting the growth and development of leaves and reducing the accumulation of nutrients in fruits. Shading significantly reduced fruit weight, sugar content, and vitamin C content at maturity and significantly increased acid content. Transcriptomic data demonstrated that low-light stress produces a large number of differential genes related to carbon metabolism, organic acid metabolism, and stress resistance, thereby suggesting that low-light stress may affect the expression of these related genes and inclusions in the fruit. The results of this study will provide theoretical and technical support for the physiological response mechanism of low-light tolerance in sweet cherry, the selection and breeding of low-light tolerant sweet cherry varieties, and the cultivation of sweet cherry in facilities.

The role of tree size, wood anatomical and leaf stomatal traits in shaping tree hydraulic efficiency and safety in a South Asian tropical moist forest

The role of tree size, wood anatomical and leaf stomatal traits in shaping tree hydraulic efficiency and safety in a South Asian tropical moist forest

Coarse woody debris legacies and their dynamics in retained forest patches

Retaining trees in small patches at final harvest is a common forest conservation measure to maintain structural and biological diversity through the young forest phase. Long-term studies of coarse woody debris (CWD, breast height diameter ≥ 10 cm) changes in retention patches remain uncommon, especially in relation to different types of patches with varying tree species composition, ground moisture, size, shape, and exposure. In the present study we re-inventoried CWD three times (1–3, 5–7 and 18–20 years after harvesting) in 60 small tree retention patches (0.03–0.54 ha) of six commonly created retention patch types, in central boreal Sweden. Most retention patch types, despite being very small (<0.55 ha) and exposed, did not experience severe tree mortality and input of CWD over the two decades. Average total volumes of CWD did not change significantly over time, although volumes of downed CWD generally increased whilst standing CWD decreased. Volumes of different decay classes were dynamic over time, but all retention types supported a variety of decay stages after 18–20 years. The volume of CWD varied significantly between the six retention patch types, with buffer zones to mire having the lowest average volume of 9 m3 ha−1 and buffer zones to rocky outcrop the highest average volume of 32 m3 ha−1, when summarised over the whole study period. Very few patch-level environmental variables (except type) related to the amount of CWD in retention patches; only the retained living tree volume of patches during creation was clearly positively correlated with higher post-harvest CWD volumes. Patch characteristics such as size and shape index did not relate to the CWD volumes in retention patches, and patch exposure only related to higher CWD volumes within the first 1–3 years after harvest. Retention patches generally supported a variety of living trees, CWD volumes and qualities over time. Several retention patch types; such as free-standing coniferous and deciduous patches, rocky outcrop buffers, wet forest patches and buffers to water, supported average CWD volumes between 19–41 m3 ha−1 after 18–20 years, under remaining canopy cover. Our findings challenge the traditional management principles aimed at minimizing severe windthrow and CWD input (i.e., creating larger patches (>0.5–1 ha), choosing topographically sheltered areas, selecting specific tree species and ground conditions). However, our study was too small in scale to investigate multiple within-patch-type interacting environmental variables. Future larger-scale studies over extended time periods are needed to disentangle such interactions for the dynamics of CWD and associated biodiversity in retention patches.

Relationship between species diversity and tree size in natural forests around the Tropic of Cancer

Although numerous hypotheses have been proposed to explain the patterns of species diversity of forests at local and landscape levels, it is still difficult to predict the alpha diversity of species, especially in tropical and subtropical natural forests where trees of different sizes and shapes are highly mixed. Size might characterize species diversity, and the possible correlation between these variables may contribute to the development of easy-to-use growth indicators to predict diversity and to understand the status of trees within a stand. In this study, diameter classes were divided using the equal diameter class (EDC) and minimum measured diameter (MMD) methods, and five species diversity indices were calculated for each diameter class of 14 permanent plots in five national nature reserves surrounding the Tropic of Cancer (23.5°), southwest China. The results show that species richness, abundance, and spatial diversity indices decreased in a typical inverted J-shape pattern with increasing diameter class and MMD, and could be easily modeled by a negative exponential function. The Shannon–Wiener index showed a linear decrease while Pielou’s evenness index displayed a linear increase, with a small degree of instability. The results suggest that species diversity in subtropical forests is closely related to tree size, and the relationship is possibly independent of habitat. Measuring DBH of some trees in a stand could be informative regarding species diversity and contribute to the investigation and assessment of biodiversity.

Statistical summaries of unlabelled evolutionary trees.

Rooted and ranked phylogenetic trees are mathematical objects that are useful in modelling hierarchical data and evolutionary relationships with applications to many fields such as evolutionary biology and genetic epidemiology. Bayesian phylogenetic inference usually explores the posterior distribution of trees via Markov chain Monte Carlo methods. However, assessing uncertainty and summarizing distributions remains challenging for these types of structures. While labelled phylogenetic trees have been extensively studied, relatively less literature exists for unlabelled trees that are increasingly useful, for example when one seeks to summarize samples of trees obtained with different methods, or from different samples and environments, and wishes to assess the stability and generalizability of these summaries. In our paper, we exploit recently proposed distance metrics of unlabelled ranked binary trees and unlabelled ranked genealogies, or trees equipped with branch lengths, to define the Fréchet mean, variance and interquartile sets as summaries of these tree distributions. We provide an efficient combinatorial optimization algorithm for computing the Fréchet mean of a sample or of distributions on unlabelled ranked tree shapes and unlabelled ranked genealogies. We show the applicability of our summary statistics for studying popular tree distributions and for comparing the SARS-CoV-2 evolutionary trees across different locations during the COVID-19 epidemic in 2020. Our current implementations are publicly available at https://github.com/RSamyak/fmatrix.

Geomatic Data Fusion for 3D Tree Modeling: The Case Study of Monumental Chestnut Trees

In recent years, advancements in remote and proximal sensing technology have driven innovation in environmental and land surveys. The integration of various geomatics devices, such as reflex and UAVs equipped with RGB cameras and mobile laser scanners (MLS), allows detailed and precise surveys of monumental trees. With these data fusion method, we reconstructed three monumental 3D tree models, allowing the computation of tree metric variables such as diameter at breast height (DBH), total height (TH), crown basal area (CBA), crown volume (CV) and wood volume (WV), even providing information on the tree shape and its overall conditions. We processed the point clouds in software such as CloudCompare, 3D Forest, R and MATLAB, whereas the photogrammetric processing was conducted with Agisoft Metashape. Three-dimensional tree models enhance accessibility to the data and allow for a wide range of potential applications, including the development of a tree information model (TIM), providing detailed data for monitoring tree health, growth, biomass and carbon sequestration. The encouraging results provide a basis for extending the virtualization of these monumental trees to a larger scale for conservation and monitoring.

Effect of Branch Bending on the Canopy Characteristics and Growth of Peach (Prunus persica (L.) Batsch)

A reasonable main branch opening angle can improve the canopy light environment of a tree, change the direction of nutrient transport, and promote the formation of flower buds. In this experiment, 3-year-old ‘Lu Hong 618’ was used as the test material to study the effects of different main branch opening angles (three treatments: 45°, 65°, and 85°) on the canopy light distribution, canopy characteristics, fruit quality, and flower bud quality of ‘Y’-shaped peach trees. The main findings were as follows: the solar energy utilization in the canopy varied greatly between different main branch opening angles, with the best relative light intensity of the canopy at 85°. In addition, the canopy light distribution on photosynthesis was more reasonable at 85°, and the daily variation range of CO2 concentration in the inner canopy was the greatest, which facilitated ventilation and light penetration in the inner canopy. With the increase in the main branch opening angle, the new growth of peach trees and the growth of the main branch trunk were inhibited. A reasonable branch opening angle results in good branch structure and leaf morphology. Leaf stomatal morphology and the soluble sugar and starch contents at different levels of the canopy are influenced by canopy light, and higher levels of canopy light can significantly increase the stomatal size and improve the leaf photosynthetic capacity, SPAD value, and soluble sugar and starch contents. With the increase in the main branch opening angle, C/N tended to increase. In addition, the distribution pattern of fruit quality in the canopy was similar to that of light distribution. In the same fruiting part, the fruit quality was higher at 85° and 45° than at 65° and slightly higher at 85° than at 45°, but the difference was not significant. The effects of different main branch opening angle treatments on the fruit weight, flesh firmness, soluble solids, and titratable acid were more significant. The 85° pulling angle effectively increased the light intensity of the different canopy layers of the peach trees and promoted the accumulation of nutrients. An 85° pulling angle can be used as a more suitable pulling angle for peach tree shaping cultivation.

Optimal bucking of stems from terrestrial laser scanning data to maximize forest value

ABSTRACT An optimal bucking strategy that allocates cutting patterns to forest stands based on the individual characteristics of each stem is critical for maximizing value recovery. However, cutting patterns are usually excluded from bucking algorithms due to the difficulties associated with capturing tree quality features when collecting forest inventory data (e.g. branchiness and tree shape). This paper presents a non-destructive and fully automated methodology for the optimal bucking of stems based on terrestrial laser scanning (TLS) point clouds that aims to maximize the economic value of trees in a forest stand. It is based on the three-dimensional modelling of stems and includes the diameter and curvature of each log. The bucking algorithm also considers several timber products and calculates the most valuable log combination for each tree. The methodology was tested in a Pinus radiata plot with 120 trees, and the results were compared with those obtained with input data that do not take curvature into account: i.e. only diameters from TLS and taper equations. The analysis of the results suggests that not including curvature in the algorithm for optimal bucking results in an overestimation of the commercial value of timber products.

Signatures of natural selection in tree topology shape of serially sampled viral phylogenies

Tree shape metrics can be computed fast for trees of any size, which makes them promising alternatives to intensive statistical methods and parameter-rich evolutionary models in the era of massive data availability. Previous studies have demonstrated their effectiveness in unveiling important parameters in viral evolutionary dynamics, although the impact of natural selection on the shape of tree topologies has not been thoroughly investigated. We carried out a forward-time and individual-based simulation to investigate whether tree shape metrics of several kinds could predict the selection regime employed to generate the data. To examine the impact of the genetic diversity of the founder viral population, simulations were run under two opposing starting configurations of the genetic diversity of the infecting viral population. We found that four evolutionary regimes, namely, negative, positive, and frequency-dependent selection, as well as neutral evolution, were successfully distinguished by tree topology shape metrics. Two metrics from the Laplacian spectral density profile (principal eigenvalue and peakedness) and the number of cherries were the most informative for indicating selection type. The genetic diversity of the founder population had an impact on differentiating evolutionary scenarios. Tree imbalance, which has been frequently associated with the action of natural selection on intrahost viral diversity, was also characteristic of neutrally evolving serially sampled data. Metrics calculated from empirical analysis of HIV datasets indicated that most tree topologies exhibited shapes closer to the frequency-dependent selection or neutral evolution regimes.

Characterization and selection of thin-shelled walnut (Juglans regia L.) genotypes of Mustang, Nepal

Walnut (Juglans regia L.) of seedling origin creates large variability within this crop. A research study was carried out at Directorate of Agricultural Research, Lumle, Kaski and Marpha, Mustang to characterize and deciphers the variability of thin-shelled walnut for further selection, conservation and variety registration. Walnut orchard of Mustang district was surveyed in March, 2018 and 50 walnut trees were labeled according to its flowering and flushing time. 36 accessions of thin-shelled walnut were characterized on 17 different parameters regarding growth habit, bearing habit, fruit and kernel characteristics. Around 88.89% trees exhibited terminal fruiting habit and remaining showed lateral fruiting habit. Three type of tree shape was noticed as spreading round, semi-erect and erect. Huge variation in nut shape was observed having 50% trees were with circular nuts. Four types of shell strength was recorded; 11.11% accessions having papery shell, 27.78% having weak shell, 47.22% having intermediate shell and 13.88 having strong shell strength. Average nut yield of trees ranged from 15-75 kg with an average of 26.67 kg. Nut weighted from 5.96-18.99 g with an average of 11.14 g. Kernel weight ranged from 2.8-8.92 g. More than 50% shelling was recorded in 13 accessions. The kernel quality of 14 accessions (out of 36) showed 5 rank (Excellent quality); and remaining 22 accessions showed 4 rank (Good quality). Based on this characterization, 13 accessions were selected and recommended for further multiplication and variety registration.

Comparing mobile and terrestrial laser scanning for measuring and modelling tree stem taper

Abstract Measuring and modelling the shape of tree stems is a fundamental component of forest inventory systems for both commercial and biological purposes. The change in diameter of the stem along its length (a.k.a. 'taper') is one of the most important and widely used means of predicting tree stem volume. Until recently, the options for obtaining accurate estimates of stem taper and developing stem taper models have been limited to measurements of felled trees or the use of optical dendrometers on standing live trees. Here, we tested both a tripod-mounted terrestrial laser scanner (TLS; a Focus 3D 120 of FARO Technologies, Inc., Lake Mary, FL, USA), and a mobile laser scanner (MLS; the ZEB1 of the GeoSLAM Ltd, Nottingham, UK) to measure tree diameters at various heights along the stem of 20 destructively harvested broadleaf and needleleaf species using the outer hull modelling method, for the purpose of developing individual-tree and species-specific taper models. Laser scanner specifications were a major factor determining stem taper measurement accuracy. The longer-range, low beam divergence TLS could estimate stem diameter to an average of 15.7 m above ground (about 79 per cent of the canopy height), while the shorter-range high beam divergence MLS could estimate an average of 11.5 m above ground (about 45 per cent of the canopy height). Stem taper error increased with respect to height above ground, with the TLS providing more consistent and reliable diameter measurements (root mean square error (RMSE) = 1.93 cm; 9.57 per cent) compared with the MLS (RMSE = 2.59 cm; 12.84 per cent), but both methods were nearly unbiased. We attribute ~60 per cent of the uncertainty in stem measurements to laser beam diameter and point density, showing positive and negative correlations, respectively. MLS was unable to converge on the two tested taper models but was found to be an efficient means of easily sampling diameters at breast height (DBH) and reconstructing stem maps in simple forest stands with trees greater than ~10 cm DBH. TLS provided precision stem diameter measurements that allowed for the creation of similar taper models for three out of the four study species. Future work should focus on evaluating MLS systems with improved specifications (e.g. beam divergence and range), since these instruments will likely lead to dramatic improvements in reliable estimates of forest inventory parameters, in line with the current TLS technology.

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Impact of genome and epigenome on intratumor heterogeneity in colorectal cancer

Insights on the stem elongation of spur-type bud sport mutant of ‘Red Delicious’ apple

The decreased capacity of auxin-, CTK-, and BR-mediated cell division and cell enlargement pathways, combined with the enhanced capacity of GA and ETH-, JA-, ABA-, SA-mediated stress-resistant pathways were presumed to be the crucial reasons for the formation of spur-type 'Red Delicious' mutants. Vallee Spur', which exhibit short internodes and compact tree shape, is the fourth generation of the spur-type bud sport mutant of 'Red Delicious'. However, the underlying molecular mechanism of these properties remains unclear. Here, comparative phenotypic, full-length transcriptome and phytohormone analyses were performed between 'Red Delicious' (NSP) and 'Vallee Spur' (SP). The new shoot internode length of NSP was ˃ 1.53-fold higher than that of the SP mutant. Cytological analysis showed that the stem cells of the SP mutant were smaller and more tightly arranged relative to the NSP. By Iso-Seq, a total of 1426 differentially expressed genes (DEGs) were detected, including 808 upregulated and 618 downregulated genes in new shoot apex with 2 leaves of the SP mutant. Gene expressions involved in auxin, cytokinin (CTK), and brassinosteroid (BR) signal transduction were mostly downregulated in the SP mutant, whereas those involved in gibberellin (GA), ethylene (ETH), jasmonate (JA), ABA, and salicylic acid (SA) signal transduction were mostly upregulated. The overall thermogram analysis of hormone levels in the shoot apex carrying two leaves detected by LC-MS/MS absolute quantification showed that the levels of IAA-Asp, IAA, iP7G, OPDA, and 6-deoxyCS were significantly upregulated in the SP mutant, while the remaining 28 hormones were significantly downregulated. It is speculated that the decreased capacity of auxin, CTK, and BR-mediated cell division and cell enlargement pathways is crucial for the formation of the SP mutant. GA and stress-resistant pathways of ETH, JA, ABA, and SA also play vital roles in stem elongation. These results highlight the involvement of phytohormones in the formation of stem elongation occurring in 'Red Delicious' spur-type bud sport mutants and provide information for exploring its biological mechanism.

Oncogenetic pedigrees: Relation between design and ability to predict mutation

We consider the risk of a disease caused by the presence within the genome of one deleterious mutation or two interacting mutations. For an individual, the probability of being mutated/doubly mutated can be estimated by knowing the phenotype of the other members in the family pedigree. We study the performance of this process as a function of the size, the shape of the family tree and the parameters of the model. We carry out simulations using the parameters pertaining to breast/ovarian cancer in BRCA-mutated families.