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Based on 1038 knots from 42 sample trees from 14 standard plots in Korean pine (Pinus koraiensis Sieb. et Zucc.) plantations in Heilongjiang Province, China, we developed a knot profile model system. The concepts of growth inflection point and death inflection point were proposed. Depending on the growth conditions near the growth inflection point of the knot, we divided the knots into two types: curved knots and linear knots. A logistic regression model was constructed to predict the shape of the knots. The area under the curve of the logistic regression model was 0.699 (95% confidence interval 0.661~0.736), and the prediction accuracy was 0.69. Our research shows that for middle-aged and young forests, the relative radial distances of the growth inflection points at the upper edge and bottom edge of curved knots were larger than those in linear knots. The curved knots did not bend at the death inflection point, but linear knots may bend at the death inflection point. Models were constructed separately for curved knots and linear knots. The results showed that the application of the mixed- effects model significantly improves the model fitting effect. Key words: Korean pine plantation, mixed-effects model, knot profile, growth inflection point, death inflection point. A partir de 1 038 noeuds de 42 arbres d'echantillonnage de 14 parcelles standard de pins de la Coree (Pinus koraiensis Sieb. et Zucc.) dans la province de Heilongjiang, en Chine, nous avons developpe un systeme de modele de profil de noeud. Les concepts de point d'inflexion de la croissance et de point d'inflexion de la mort ont ete proposes. Selon les conditions de croissance proche du point d'inflexion de la croissance du noeud, nous avons divise les noeuds en deux types : noeuds courbes et noeuds lineaires. Un modele de regression logistique a ete elabore pour prevoir la forme des noeuds. La surface sous la courbe (SSC) du modele de regression logistique etait de 0,699 (95 % de la zone d'incertitude de mesure de 0,661~0,736) et la precision de la prevision etait de 0,69. La recherche indique que pour les jeunes forets et les forets d'age moyen, les distances radiales relatives des points d'inflexion de la croissance du bord superieur et du bord inferieur des noeuds courbes etaient plus larges que ceux des noeuds lineaires. Les noeuds courbes ne pliaient pas au point d'inflexion de la mort, mais les noeuds lineaires pouvaient plier au point d'inflexion de la mort. Les modeles ont ete elabores separement pour les noeuds courbes et les noeuds lineaires. Les resultats ont indique que l'application du modele d'effets contrastes ameliore considerablement l'effet d'ajustement du modele. [Traduit par la Redaction] Mots-cles : plantation de pins de la Coree, modele d'effets contrastes, profil du noeud, point d'inflexion de la croissance, point d'inflexion de la mort., 1. Introduction Knots are one of the most important characteristics affecting the quality and value of wood (Gartner 2005), as they reduce the continuity of wood fibers and the strength [...]

Background: The Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families. Methods: Here, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated. Results: The mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period. Conclusions: This study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder. [ABSTRACT FROM AUTHOR]

Background: Despite the Caridean shrimps' vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes. Methods: The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina's next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results: The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species—P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions: Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus. [ABSTRACT FROM AUTHOR]

Crown vertical profiles (CVP) play an essential role in stand biomass and forest fire prediction. Traditionally, due to measurement difficulties, CVP models developed based on a small number of individual trees are not convincing. Terrestrial laser scanning (TLS) provides new insights for researching trees' CVPs. However, there is a limited understanding of the ability to accurately describe CVPs with TLS. In this study, we propose a new approach to automatically extract the crown radius (CR) at different heights and confirm the correctness and effectiveness of the proposed approach with field measurement data from 30 destructively harvested sample trees. We then applied the approach to extract the CR from 283 trees in 6 sample plots to develop a two-level nonlinear mixed-effects (NLME) model for the CVP. The results of the study showed that the average extraction accuracy of the CR when the proposed approach was applied was 90.12%, with differences in the extraction accuracies at different relative depths into the crown (RDINC) ranges. The TLS-based extracted CR strongly correlated with the field-measured CR, with an R2 of 0.93. Compared with the base model, the two-level NLME model has significantly improved the prediction accuracy, with Ra2 increasing by 13.8% and RMSE decreasing by 23.46%. All our research has demonstrated that TLS has great potential for accurately extracting CRs, which would provide a novel way to nondestructively measure the crown structure. Moreover, our research lays the foundation for the future development of CVP models using TLS at a regional scale. [ABSTRACT FROM AUTHOR]

In bacteria, where gene transcription and translation occur concurrently, post-transcriptional regulation is acknowledged to be effective and precise. The 5' untranslated regions (5' UTRs) typically harbor diverse post-transcriptional regulatory elements, like riboswitches, RNA thermometers, small RNAs, and upstream open reading frames, that serve to modulate transcription termination, translation initiation, and mRNA stability. Consequently, exploring 5' UTR-derived regulatory elements is vital for synthetic biology and metabolic engineering. Over the past few years, the investigation of successive mechanisms has facilitated the development of various genetic tools from bacterial 5' UTRs. This review consolidates current understanding of 5' UTR regulatory functions, presents recent progress in 5' UTR-element design and screening, updates the tools and regulatory strategies developed, and highlights the challenges and necessity of establishing reliable bioinformatic analysis methods and non-model bacterial chassis in the future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)