Alignment Tree Research Articles

From Coarse to Fine: Non-Rigid Sparse-Dense Registration for Deformation-Aware Liver Surgical Navigation.

Intraoperative liver deformation poses a considerable challenge during liver surgery, causing significant errors in image-guided surgical navigation systems. This study addresses a critical non-rigid registration problem in liver surgery: the alignment of intrahepatic vascular trees. The goal is to deform the complete vascular shape extracted from preoperative Computed Tomography (CT) volume, aligning it with sparse vascular contour points obtained from intraoperative ultrasound (iUS) images. Challenges arise due to the intricate nature of slender vascular branches, causing existing methods to struggle with accuracy and vascular self-intersection. We present a novel non-rigid sparse-dense registration pipeline structured in a coarse-to-fine fashion. In the initial coarse registration stage, we introduce a parametrization deformation graph and a Welsch function-based error metric to enhance convergence and robustness of non-rigid registration. For the fine registration stage, we propose an automatic curvature-based algorithm to detect and eliminate overlapping regions. Subsequently, we generate the complete vascular shape using posterior computation of a Gaussian Process Shape Model. Experimental results using simulated data demonstrate the accuracy and robustness of our proposed method. Evaluation results on the target registration error of tumors highlight the clinical significance of our method in tumor location computation. Comparative analysis against related methods reveals superior accuracy and competitive efficiency of our approach. Moreover, Ex vivo swine liver experiments and clinical experiments were conducted to evaluate the method's performance. The experimental results itasize the accurate and robust performance of our proposed method. Our proposed non-rigid registration method holds significant application potential in clinical practice.

Genetic and recombination heterogeneity of canine bufaviruses detected in diarrheal dogs in China

Bufavirus (BuV) was first identified in feces from children with acute diarrhea, and a genetically related Canine bufavirus (CBuV) was first reported in Italy in 2018. In this study, through the investigation of CBuV in 622 anal swabs from dogs with diarrhea symptoms collected from various provinces in northern, central and eastern China during 2018–2022, 14 samples were detected to be positive. And 5 samples were from dogs co-infected with other canine diarrhea related viruses, which consist of CPV-2, CDV and CCoV. The complete genome sequences (4219 nt) of the fourteen strains were amplified and sequenced. Through comparative analysis with 51 reference BuV strains, six strains might recombinate from the CBuV strains (HUN/2012/22, CaBuV/9AS/2005/ITA and CaBuV/35/2016/ITA) in Hungary and Italy as the parents, and two genetic recombination events from various parents were predicted to occur on the BUV-422 strain. Combined analyzing the phylogenetic tree and sequence alignment, it was found that these CBuVs are highly conserved in the nonstructural protein NS1, but indeed various amino acid mutation sites in the capsid protein VP2, and even some amino acid sites coincide with putative protein plastic regions and potential epitopes. The BUV-422 and BUV-512 strains show sequential mutation sites identical to the divergent strains of CaBuV/9AS/2005/ITA and CaBuV/35/2016/ITA. This study would enrich the molecular data of CBuV in China and provide essential reference for the epidemiological research and vaccine development of CBuV in the future.

Molecular characterization, cytoprotective, DNA protective, and immunological assessment of peroxiredoxin-1 (Prdx1) from yellowtail clownfish (Amphiprion clarkii)

Peroxiredoxin-1 (Prdx1) is a thiol-specific antioxidant enzyme that detoxifies reactive oxygen species (ROS) and regulates the redox status of cells. In this study, the Prdx1 cDNA sequence was isolated from the pre-established Amphiprion clarkii (A. clarkii) (AcPrdx1) transcriptome database and characterized structurally and functionally. The AcPrdx1 coding sequence comprises 597 bp and encodes 198 amino acids with a molecular weight of 22.1 kDa and a predicted theoretical isoelectric point of 6.3. AcPrdx1 is localized and functionally available in the cytoplasm and nucleus of cells. The TXN domain of AcPrdx1 comprises two peroxiredoxin signature VCP motifs, which contain catalytic peroxidatic (Cp-C52) and resolving cysteine (CR-C173) residues. The constructed phylogenetic tree and sequence alignment revealed that AcPrdx1 is evolutionarily conserved, and its most closely related counterpart is Amphiprion ocellaris. Under normal physiological conditions, AcPrdx1 was ubiquitously detected in all tissues examined, with the most robust expression in the spleen. Furthermore, AcPrdx1 transcripts were significantly upregulated in the spleen, head kidney, and blood after immune stimulation by polyinosinic:polycytidylic acid (poly (I:C)), lipopolysaccharide (LPS), and Vibrio harveyi injection. Recombinant AcPrdx1 (rAcPrdx1) demonstrated antioxidant and DNA protective properties in a concentration-dependent manner, as evidenced by insulin disulfide reduction, peroxidase activity, and metal-catalyzed oxidation (MCO) assays, whereas cells transfected with pcDNA3.1(+)/AcPrdx1 showed significant cytoprotective function under oxidative and nitrosative stress. Overexpression of AcPrdx1 in fathead minnow (FHM) cells led to a lower viral copy number following viral hemorrhagic septicemia virus (VHSV) infection, along with upregulation of several antiviral genes. Collectively, this study provides insights into the function of AcPrdx1 in defense against oxidative stressors and its role in the immune response against pathogenic infections in A. clarkii.

Nothing to it: a reply to Wheeler's "much ado about nothing".

Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not in a separate absence/presence character but as insertion/deletion events in a complex character that describes the feature in all its variation; and that this dynamic homology view can be achieved by imposing a sequence or linear order on a set of characters and by analysing the resulting sequence character using custom alphabet tree alignment algorithms. As Wheeler observed, this approach can lead to considering inappropriate character states (such as a head state and a foot state) homologous. We show that it is also sensitive to the specific ordering assumption used and that such different character orders can lead to a preference for different trees. We present a simple four-taxon dataset with observations of absence, but no inapplicable characters or other kinds of character dependence, for which the dynamic homology framework gives different results to classic algorithms for independent characters, including an optimal tree with biologically impossible reconstructions at inner nodes (every terminal has a head but the inner nodes are headless). We show how these issues can be solved by removing the character ordering assumption that the approach requires. Doing so, the dynamic homology framework reduces in general to Maddison's (Syst. Biol. 1993, 42, 576) well-known proposal to deal with inapplicability using step matrix analysis of complex characters. If in addition costs are interpreted in terms of homology, it reduces to Goloboff et al.'s (Cladistics 2021, 37, 596) step matrix implementation for maximization of homology as applied to inapplicable characters. However, if used with homogeneous costs, as Wheeler suggested, it reduces to unordered analysis of such complex characters, which is known to treat tails that may share many observed features as irrelevant for establishing kinship when they differ in just one feature, e.g. colour.

Kidney cell culture of Rana dybowskii and study molecules of TRIF in Rana dybowskii cells under the stress of Aeromonas hydrophila

As a model organism, the cell culture method of Rana dybowskii (Rd) has not received widespread attention. We obtained kidney cells from Rana dybowskii by tissue block culture and enzyme digestion, and optimized the culture method by changing different culture conditions. We can more conveniently study the operation of the Rana dybowskii immune system through cell lines. One of the most important adaptor proteins in the Toll-like receptors (TLRs) signaling pathway, TIR-domain-containing adaptor inducing interferon-β (TRIF), plays a role in the apoptosis pathway and participates in the ubiquitin-mediated protein hydrolysis pathway. This rationalizes the significance of TRIF in the immune cascade signaling pathway. To obtain and analyze the full-length sequence of cDNA, sequential structures of amino acids, as well as Rana dybowskii TRIF expression profiles, the present work carried out multiple-sequence alignment, rapid amplification of cDNA ends (RACE), the establishment of a phylogenetic tree, search for the conserved domain, and qRT-PCR. Results revealed 1733-bp full-length cDNA of RdTRIF with an open reading frame (ORF) of 1281 bp, which encoded one protein containing 426 amino acid residues. The amino acid sequence of RdTRIF confirmed the presence of one Toll/interleukin-1 receptor (TIR) domain. As a kind of hydrophilic protein, the pI and molecular weight of RdTRIF were 5.67 and 24.76 kDa, respectively. We predicted 51 candidate phosphorylation sites, including 32 serine residues, 16 threonine residues along with 3 tyrosine residues. The phylogenetic tree and multiple-sequence alignment substantiated the highest homology of RdTRIF protein to Xenopus tropicalis homologs. According to the qRT-PCR results, the expression of RdTRIF was noted under the stress of Ah in the kidney.

Mutation Interest in the Receptor-Binding Domain of Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2 in the Northwest of Iran

Background: The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing variation. Most of the variants cause no concern for human health. Some others have had worse outcomes in terms of transmissibility, vaccination resistance, and, generally, the survival of patients infected with SARS-CoV-2. Objectives: This study investigated the mutation of interest in the receptor-binding domain (RBD) of SARS-CoV-2. Methods: Ribonucleic acid (RNA) was extracted from 40 swap samples. Next, the polymerase chain reaction (PCR) assay was carried out to detect the RBD. Investigation of SARS-COV-2 RBD was performed completely by phylogenetic and tree alignment. The multiple sequence alignment (MSA) of the biological sequence of RBD was created by BioEdit, Snap Gene, and MEGA software and was then compared to sequences of different variants of SARS-COV-2 in the GenBank (National Center for Biotechnology Information). The Influenza Surveillance and Response System (GSAID) was used to detect mutations in the RBD sequence. Results: Multiple sequence alignment (MSA) RBD domain showed that the RBD domain sequence obtained from the Iranian patients' highest identity by severe acute respiratory syndrome coronavirus 2 isolate MZ907347. Several mutations of interest, including A475V, L452R, V483A, and F490L, were detected in the RBD region. However, the dN/dS analysis detected positive selection in RBD regions. Conclusions: Amino acid changes in the surface protein can significantly alter the viral function and/or interactions with neutralizing antibodies. Most of the nucleotide changes in the spike gene reduce infectivity. The V503W and P521Q mutations reduce infectivity, the A522Q mutation increases sensitivity to neutralizing antibodies, and the H519T mutation decreases susceptibility to convalescent sera.

Immunochemical Characterization of Salix alba (S. alba) Pollen Allergens and Evaluation of the Cross-Reactivity Pattern with Common Allergenic Pollen Grains

BackgroundPollens, particularly tree and plant pollens, are one of the major causes of allergic respiratory diseases worldwide. Allergy to pollens of different species of Salix trees has been reported in various regions of the world. The most common type of Salix tree in Iran is white willow (Salix alba). ObjectivesThis study aimed to identify and determine the immunochemical characteristics of allergenic proteins in S. alba tree pollen extract using SDS-PAGE and IgE- immunoblotting methods. Moreover, the cross-reaction pattern of the specific IgE antibody of S. alba tree pollen proteins with pollen allergens of common allergenic trees, i.e., Populus nigra (P. nigra), Cupressus sempervirens (C. sempervirens), Pinus brutia (P. brutia) and Platanus orientalis (P. orientalis) in the region was investigated. MethodsThe reaction of allergenic proteins in S. alba pollen extract with specific IgE antibodies in patients' sera was investigated using SDS-PAGE and IgE-immunoblotting methods. The cross-reaction of specific IgE antibodies of the proteins present in S. alba pollen extract with pollen allergens of common allergenic trees in the region was investigated using ELISA and immunoblotting inhibition methods. In silico methods such as phylogenetic tree drawing and alignment of amino acid sequences were used to examine the evolutionary relationship and homology structure of common allergenic proteins (Panallergens) responsible for cross reactions. ResultsMore than 11 protein bands binding to specific IgE antibodies in patients' sera with a molecular weight between 13 and 95 kDa were identified in the S. alba tree pollen extract. ELISA and immunoblotting inhibition results showed that P. nigra extract could inhibit the binding of IgE antibodies to S. alba pollen extract proteins to a greater extent than C. sempervirens, P. brutia, and P. orientalis tree extracts. In silico methods investigated the results of ELISA and immunoblotting inhibition methods. Moreover, a high structural homology and evolutionary relationship were observed between S. alba and P. nigra tree pollen panallergens. ConclusionIn this study, it was found that more than 80 % of the sensitive patients who were examined had specific IgE antibodies reacting with the approximately a 15 kDa-protein present in the S. alba pollen extract. Furthermore, the specific IgE-binding proteins found in the pollens of S. alba and P. nigra trees had relative structural homology, and it is likely that if recombinant forms are produced, they can be used for diagnostic and therapeutic purposes for both of the trees.

Molecular characterization of four genes encoding abalone insulin-related peptides and their roles in regulation of hemolymph glucose in the Pacific abalone Haliotis discus hannai

Members of the insulin superfamily play key roles in metabolism, growth, reproduction, and longevity via insulin/IGF signaling pathway. The presence of insulin and insulin-related peptides are found among animals. In Mollusca, molluscan insulin-related peptides (MIPs) are involved in their body and shell growth. Hence, this study aimed to understand if there was difference in these peptide levels of fast and slow growing Pacific abalones, Haliotis discus hannai. To this end, four abalone insulin-related peptides (AIPs) are mined from cerebral ganglia transcriptomes of fast-growing and slow-growing abalones: AIP1, −2, −3 and −6. Notably, these AIPs possess 8 cysteine residues in their predicted insulin A and B chains, potentially supporting four disulfide bridges. Further sequence analysis based on the phylogenetic tree and multiple alignment methods indicated that AIPs have sequence features that are conserved among MIPs in many gastropods. The tissue distributions of four AIPs showed ubiquitous and similar expression in the following tissues including the cerebral ganglion, hepatopancreas, gonad, and mantle of both genders. However, there is some difference in other tissue distribution. Since the food consumption is intimately associated with the hemolymph glucose and animal growth, relative AIP1, −2, −3 and − 6 expression levels in the cerebral ganglion were measured following seaweed supplementation. The animals fed with brown seaweed showed increased these AIPs by 1.6–4.7 folds from 3 h after feeding, which lasting to 12 h, coinciding with the peak of hemolymph glucose. Based on these results, we propose that a physiological glucose regulatory mechanism involving AIPs exists in the cerebral ganglion of the H. discus hannai neuroendocrine system.

Ultrafast Ultrasound Vector Doppler for Small Vasculature Imaging.

Ultrafast Doppler has been accepted as a novel modality for small vasculature imaging with high sensitivity, high spatiotemporal resolution and high penetration. However, conventional Doppler estimator adopted in studies of ultrafast ultrasound imaging is only sensitive to the velocity component along the beam direction and has angle-dependent limitation. Vector Doppler has been developed with the goal of angle-independent velocity estimation, but is typically employed for relatively large vessels. In this study, combining multiangle vector Doppler strategy and ultrafast sequencing, ultrafast ultrasound vector Doppler (ultrafast UVD) is developed for small vasculature hemodynamic imaging. The validity of the technique is demonstrated through experiments on a rotational phantom, rat brain, human brain and human spinal cord. A rat brain experiments show that compared with the ultrasound localization microscopy (ULM) velocimetry, which is widely accepted as an accurate flow velocimetry technique, the average relative error (ARE) of the velocity magnitude estimated by ultrafast UVD is approximately 16.2%, with an RMSE of the velocity direction of 26.7°. It is demonstrated that ultrafast UVD is a promising tool for accurate blood flow velocity measurement, especially for the organs including brain and spinal cord with vasculature typically exhibiting tendential alignment of vascular trees.

A Method for Predicting Canopy Light Distribution in Cherry Trees Based on Fused Point Cloud Data

A proper canopy light distribution in fruit trees can improve photosynthetic efficiency, which is important for improving fruit yield and quality. Traditional methods of measuring light intensity in the canopy of fruit trees are time consuming, labor intensive and error prone. Therefore, a method for predicting canopy light distribution in cherry trees was proposed based on a three-dimensional (3D) cherry tree canopy point cloud model fused by multiple sources. First, to quickly and accurately reconstruct the 3D cherry tree point cloud model, we propose a global cherry tree alignment method based on a binocular depth camera vision system. For the point cloud data acquired by the two cameras, a RANSAC-based orb calibration method is used to externally calibrate the cameras, and the point cloud is coarsely aligned using the pose transformation matrix between the cameras. For the point cloud data collected at different stations, a coarse point cloud alignment method based on intrinsic shape signature (ISS) key points is proposed. In addition, an improved iterative closest point (ICP) algorithm based on bidirectional KD-tree is proposed to precisely align the coarse-aligned cherry tree point cloud data to achieve point cloud data fusion and obtain a complete 3D cherry tree point cloud model. Finally, to reveal the pattern between the fruit tree canopy structure and the light distribution, a GBRT-based model for predicting the cherry tree canopy light distribution is proposed based on the established 3D cherry tree point cloud model, which takes the relative projected area features, relative surface area and relative volume characteristics of the minimum bounding box of the point cloud model as inputs and the relative light intensity as output. The experiment results show that the GBRT-based model for predicting the cherry tree canopy illumination distribution has good feasibility. The coefficient of determination between the predicted value and the actual value is 0.932, and the MAPE is 0.116, and the model can provide technical support for scientific and reasonable cherry tree pruning.

Modeling of logging machine stability operating with a vertically held tree

The article presents the results of mathematical modeling of the stability of a logging machine with a vertically held tree when it is removed from the canopy of the forest. The calculation schemes for two positions of a vertically held tree are described. The substantiation of the idealization for the calculation schemes of a vertically held tree is given. The dynamic stability equations of a logging machine with a vertically held tree are constructed on the basis of second kind Lagrange equations system. Due to analyze the interrelationships between dynamic parameters and processes of a logging machine with a vertically held tree, motion differential equations were integrated taking into account external influences and initial conditions. Using the MATLAB program, the integration operations of second kind Lagrange equations system were carried out for two cases: 1) The vertical tree is rigidly fixed and repeats the deviations of the logging machine; 2) The tree is perfectly held vertically with any deviations of the logging machine. The input parameters for the calculation were the rigidity of the connections, the parameters of the logging machine, the gripping cutting device (GCD) and the tree. The parameters of the slope of the logging machine were set using the implementation of a Gaussian random process with a given correlation and variance. The dynamic stability study of a logging machine with a vertical tree showed that the ideal tree alignment in a vertical position leads to a decrease in the inertia moment of the system and to a significant decrease in the frequency of angular and linear oscillations compared with a rigidly fixed tree.

First molecular detection and genetic analysis of porcine circovirus 4 in the Southwest of China during 2021-2022.

Porcine circovirus 4 (PCV4) was identified in 2019 as a novel circovirus species and then proved to be pathogenic to piglets. However, there is a lack of its prevalence in the Southwest of China. To investigate whether PCV4 DNA existed in the Southwest of China, 374 samples were collected from diseased pigs during 2021-2022 and detected by a real-time PCR assay. The results showed that the positive rate of PCV4 was 1.34% (5/374) at sample level, and PCV4 was detected in two of 12 cities, demonstrating that PCV4 could be detected in pig farms in the Southwest of China, but its prevalence was low. Furthermore, one PCV4 strain (SC-GA2022ABTC) was sequenced in this study and shared a high identity (98.1-99.7%) with reference strains at the genome level. Combining genetic evolution analysis with amino acid sequence analysis, three genotypes PCV4a, PCV4b, and PCV4c were temporarily identified, and the SC-GA2022ABTC strain belonged to PCV4c with a specific amino acid pattern (239V for Rep protein, 27N, 28R, and 212M for Cap protein). Phylogenetic tree and amino acid alignment showed that PCV4 had an ancient ancestor with mink circovirus. In conclusion, the present study was the first to report the discovery and the evolutionary analysis of the PCV4 genome in pig herds of the Southwest of China and provide insight into the molecular epidemiology of PCV4.

Genome-wide identification and effect of MdPEPC family genes during axillary bud outgrowth in apple (Malus domestica Borkh.)

The PEPC family proteins are ubiquitous in various plants and play an important role in the process of photosynthetic carbon assimilation and have many non-photosynthetic biological functions. However, PEPC genes have not been reported in apple. In this study, the members of apple MdPEPC family were identified based on the new apple genome data by bioinformatics analysis, and their expression patterns in different tissues and the apple axillary bud transcriptome treated by decapitation and TDZ (cytokinin) were analyzed in order to explore the role of MdPEPC genes in apple axillary bud outgrowth. The results showed that 6 MdPEPC family members were identified in apple, which distributed on 6 different chromosomes, and had similar physicochemical characteristics. Phylogenetic tree and sequence alignment analysis showed that the MdPEPC could be divided into two subgroups (Group Ⅰ and Group Ⅱ), in which four members in MdPEPC family were clustered into Group Ⅰ, belonging to plant-type PEPCs. However, MdPEPC4 and MdPEPC5 were clustered into Group Ⅱ with AtPPC4, belonging to bacterial-type PEPCs. There were 7 pairs of fragments repeats among MdPEPC members, but no tandem repeats existed. The promoter cis-acting element analysis showed that MdPEPC genes were not only affected by light and stress, but also regulated by multiple hormones. The expression profiles showed that all MdPEPCs except MdPEPC4 and MdPEPC5 were expressed in different apple tissues. Transcriptome data analysis showed that the expression levels of MdPEPC1 and MdPEPC3 were up-regulated after decapitation and TDZ treatment, whereas MdPEPC2 was significantly down-regulated at 48 h after treatments. In conclusion, MdPEPC1, MdPEPC2 and MdPEPC3 were selected as the candidate genes involved in axillary bud outgrowth regulation for further study.

Alignment of single-cell trajectory trees with CAPITAL

Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing tools mainly focus on linear alignment of single-cell trajectories. Here we present CAPITAL (comparative analysis of pseudotime trajectory inference with tree alignment), a method for comparing single-cell trajectories with tree alignment whereby branching trajectories can be automatically compared. Computational tests on synthetic datasets and authentic bone marrow cells datasets indicate that CAPITAL has achieved accurate and robust alignments of trajectory trees, revealing various gene expression dynamics including gene–gene correlation conservation between different species.

Semi-Automatic Alignment of Multilingual Parts of Speech Tagsets

We cast the problem of mapping a pair of Parts of Speech (POS) tagsets as a labelled tree mapping problem and present a general-purpose semi automatic POS tree alignment algorithm to solve the alignment. This algorithm can be used to align two POS tagsets of different languages or the same language. We evaluate its usefulness using POS tagsets of two languages: Tamil and Sinhala. The proposed approach shows that manual effort in prior approaches is drastically reduced due to the proposed algorithm and eliminates the need to create new POS tagsets.

Analysis of SARS-CoV-2 Variant of Concern Mutations in West Virginia

The SARS-CoV-2 virus, which causes COVID-19, has led to a pandemic that has impacted the world for over two years. With new variants and mutations on the rise, the objective of this project was to determine how the variants of concern (VOC) that were discovered in West Virginia differed from the original SARS-CoV-2 strain found in Wuhan, China. Using the NCBI SARS-CoV-2 database, sequences were selected and sorted based on the location of the mutation in the genomic sequence. Complete nucleotide sequences of the surface glycoproteins from West Virginia patients were identified. These sequences were then compared to the first recorded accession of each VOC in the NCBI database. The genomic sequences were analyzed, and a phylogenetic tree and protein alignment of each VOC were produced. The preliminary results show that all four of the VOCs shared more than 99% similarity with the reference sequence.

Decorated merge trees for persistent topology

This paper introduces decorated merge trees (DMTs) as a novel invariant for persistent spaces. DMTs combine both $$\pi _0$$ and $$H_n$$ information into a single data structure that distinguishes filtrations that merge trees and persistent homology cannot distinguish alone. Three variants on DMTs, which emphasize category theory, representation theory and persistence barcodes, respectively, offer different advantages in terms of theory and computation. Two notions of distance—an interleaving distance and bottleneck distance—for DMTs are defined and a hierarchy of stability results that both refine and generalize existing stability results is proved here. To overcome some of the computational complexity inherent in these distances, we provide a novel use of Gromov-Wasserstein couplings to compute optimal merge tree alignments for a combinatorial version of our interleaving distance which can be tractably estimated. We introduce computational frameworks for generating, visualizing and comparing decorated merge trees derived from synthetic and real data. Example applications include comparison of point clouds, interpretation of persistent homology of sliding window embeddings of time series, visualization of topological features in segmented brain tumor images and topology-driven graph alignment.

Genome-wide characterization of nuclear factor Y transcription factors in Fagopyrum tataricum.

The nuclear factor Y (NF-Y) is an important transcription factor family that regulates plant developmental processes and abiotic stress responses. Currently, genome-wide studies of the NF-Y family are limited in Fagopyrum tataricum, an important economic crop. Based on the released genome assembly, we predicted a total of 38 NF-Y encoding genes (FtNF-Ys), including 12 FtNF-YAs, 18 FtNF-YBs, and eight FtNF-YCs subunits, in F. tataricum. Phylogenetic tree and sequence alignments showed that FtNF-Ys were conserved between F. tataricum and other species. Tissue expressions and network analyses suggested that FtNF-Ys might be involved in regulating developmental processes in different tissues. Several FtNF-YAs and FtNF-Ybs were also potentially involved in light response. In addition, FtNF-YC-like1 and FtNF-YC-like2 partially rescued the late flowering phenotype in nf-yc1 nf-yc3 nf-yc4 nf-yc9 (ycQ) mutant in Arabidopsis thaliana, supporting a conserved role of FtNF-Ys in regulating developmental processes. Together, the genomic information provides a comprehensive understanding of the NF-Y transcription factors in F. tataricum, which will be useful for further investigation of their functions in F. tataricum.

Investigating the Viral Suppressor HC-Pro Inhibiting Small RNA Methylation through Functional Comparison of HEN1 in Angiosperm and Bryophyte.

In plants, HEN1-facilitated methylation at 3′ end ribose is a critical step of small-RNA (sRNA) biogenesis. A mutant of well-studied Arabidopsis HEN1 (AtHEN1), hen1-1, showed a defective developmental phenotype, indicating the importance of sRNA methylation. Moreover, Marchantia polymorpha has been identified to have a HEN1 ortholog gene (MpHEN1); however, its function remained unfathomed. Our in vivo and in vitro data have shown MpHEN1 activity being comparable with AtHEN1, and their substrate specificity towards duplex microRNA (miRNA) remained consistent. Furthermore, the phylogenetic tree and multiple alignment highlighted the conserved molecular evolution of the HEN1 family in plants. The P1/HC-Pro of the turnip mosaic virus (TuMV) is a known RNA silencing suppressor and inhibits HEN1 methylation of sRNAs. Here, we report that the HC-Pro physically binds with AtHEN1 through FRNK motif, inhibiting HEN1’s methylation activity. Moreover, the in vitro EMSA data indicates GST-HC-Pro of TuMV lacks sRNA duplex-binding ability. Surprisingly, the HC-Pro also inhibits MpHEN1 activity in a dosage-dependent manner, suggesting the possibility of interaction between HC-Pro and MpHEN1 as well. Further investigations on understanding interaction mechanisms of HEN1 and various HC-Pros can advance the knowledge of viral suppressors.

The simulation of the impact of the spatial distribution of vegetation on the urban microclimate: A case study in Mostaganem

Increasing vegetation is one of the solutions proposed to mitigate the phenomenon of urban heat islands. The present research aims to study the effect of the spatial distribution of vegetation on the urban microclimate during the summer period. The city of Mostaganem with its Mediterranean climate was chosen as a case study. Based on meteorological data collected on a hot day in July, the study is carried out using the ENVI-met 4.4.5. Scenarios of different vegetation layouts were carried out. Air, mean radiant and surface temperatures are the microclimatic parameters that have been analyzed for each of the scenarios, and in order to study the outdoor thermal comfort, the Predicted Mean Vote (PMV) is chosen as the comfort index, it compares the average value of the votes of a large group of people on the thermal sensation scale. The study revealed that tree alignments can have a cooling effect on the city temperature close to 1.2°C. However, its impact on reducing the surface temperature can reach up to 4 °C. The introduction of vegetation on the site had the overall effect of lowering the air temperature and therefore relatively improving the level of comfort compared to the reference scenario. But, in order to reduce discomfort to an acceptable level during the day, vegetation can be simultaneously accommodated by city parameters such as urban form.