bluuebunny/crossref_metadata_2025 huggingface dataset:
A Study to Assess the Conservation Effectiveness of Nature Reserves in Hainan, China, from 2000 to 2021
Authors: Zhang Xiaoqian , Yan Min , Zhang Li , Chen Bowei
Published: June 2023

Nature reserves are special habitats established for representative plant and animal ecosystems, and it is important to strengthen the monitoring and protection of nature reserves for ecological environmental protection. In this paper, 23 typical nature reserves of different levels and types on Hainan Island were selected as the study area. The InVEST model and LandTrendr algorithm were applied in habitat quality assessment and to anthropogenic disturbances of the study area from 2000 to 2021, respectively. Finally, an assessment mode was established, coupling the habitat quality assessment and anthropogenic disturbances, to analyze the spatial and temporal conservation effectiveness of the 23 nature reserves. The results indicate that the 23 nature reserves had good overall conservation effectiveness; 21 had an excellent effectiveness rating, and 2 had a good effectiveness rating between 2000 and 2021. Three of the nature reserves, namely, Dazhoudao, Dongzhaigang and Bangxi, have become significantly more effective. Provincial nature reserves are less effective than national nature reserves in terms of conservation, and are a key concern for follow-up. The conservation effectiveness of the four provincial nature reserves—Nanwan, Qinglangang, Dongfangheilianpilu and Qilinlai—is low, and there has been no significant trend of improvement over the past 21 years. The spatial and temporal changes in the conservation effectiveness of 23 nature reserves on Hainan Island over 21 years can provide scientific data support for the development of nature reserves and departmental supervision in Hainan Province.
Effect of Waterlogging Stress on Leaf Anatomical Structure and Ultrastructure of Phoebe sheareri Seedlings
Authors: Shi Fenghou , Pan Zhujing , Dai Pengfei , Shen Yongbao , Lu Yizeng , Han Biao
Published: June 2023

Phoebe sheareri is an excellent roadside tree with a wide distribution range and high ornamental value. Excessive moisture can affect the external morphology, the microstructure, and the ultrastructure of the leaf. Little is known at present regarding the leaf structure of P. sheareri under waterlogging stress. In this paper, the external morphology of leaves, the microstructure of leaf epidermis, and the ultrastructure of mesophyll cells of P. sheareri seedlings under waterlogging stress and drainage were dynamically observed. Waterlogging stress contributed to the yellowing and wilting of P. sheareri seedling leaves, the gradual closing of leaf epidermal stomata, increasing density of leaf stomata, gradual loosening of the arrangement of leaf cell structure, and merging of leaf palisade tissue cells. Waterlogging stress forced the structure of the chloroplast membranes to blur, gradually causing swelling, and deformation, with plasmolysis occurring in severe cases. During waterlogging, the basal lamellae were disorganized, and the mitochondrial membrane structure was damaged. The damaged state of the leaves was not relieved after drainage. Waterlogging stress not only inhibited the growth of leaves, but also accelerated the closure of stomata, disordered the arrangement of palisade tissue and spongy tissue gradually, and damaged the internal organelles of mesophyll cells.
Biochar Application: A Viable and Pyrolysis Temperature Dependent Option for Enhancing Leaf Secondary Metabolites of Cyclocarya paliurus
Authors: Li Wenhao , Tian Ye , Liu Chengyu , Yang Rui , Jin Yuanyuan , Li Tong
Published: June 2023

While numerous studies have suggested that pyrolysis of the forestry residues to produce biochar and return it back for forestry use is an effective way for the utilization of forestry wastes, there have been few reports addressing the effect of pyrolysis temperature on its agronomic functions, especially the secondary metabolism of the medicinal tree. In this study, two kinds of biochar were pyrolyzed using poplar sawdust at 350 °C (C350) and 600 °C (C600), respectively, then applied as auxiliary substrate material for the cultivation of Cyclocarya paliurus seedlings in a greenhouse to study their effects on soil properties, seedling growth and the accumulation of main secondary metabolites in C. paliurus leaves. The results showed that biochar application definitely ameliorated most of the soil properties, and this improvement was further enhanced as the pyrolysis temperature of the biochar increased. Compared with the basic substrate (CK), the growth of C. paliurus seedlings increased under C600 and decreased under C350, but the application of two biochars had no significant effect on the content of the main secondary metabolites in the leaves. In contrast, the seedling growth with the direct application of poplar sawdust (C0) was significantly inhibited, while the content of secondary metabolites in the leaves increased significantly. In terms of the yield of leaf secondary metabolites, the application of biochar with high pyrolysis temperature (C600) had the highest yield, while the direct application of poplar sawdust had the lowest yield. In addition, the contents of several metabolite monomers were higher under C0 than these of the other three treatments. The results indicated a certain trade-off between the primary growth and the synthesis of leaf secondary metabolites in C. paliurus affected by different biochars and poplar sawdust application, while the accumulation of leaf secondary metabolites was generally dependent on leaf biomass.
LWSNet: A Point-Based Segmentation Network for Leaf-Wood Separation of Individual Trees
Authors: Jiang Tengping , Zhang Qinyu , Liu Shan , Liang Chong , Dai Lei , Zhang Zequn , Sun Jian , Wang Yongjun
Published: June 2023

The accurate leaf-wood separation of individual trees from point clouds is an important yet challenging task. Many existing methods rely on manual features that are time-consuming and labor-intensive to distinguish between leaf and wood points. However, due to the complex interlocking structure of leaves and wood in the canopy, these methods have not yielded satisfactory results. Therefore, this paper proposes an end-to-end LWSNet to separate leaf and wood points within the canopy. First, we consider the linear and scattering distribution characteristics of leaf and wood points and calculate local geometric features with distinguishing properties to enrich the original point cloud information. Then, we fuse the local contextual information for feature enhancement and select more representative features through a rearrangement attention mechanism. Finally, we use a residual connection during the decoding stage to improve the robustness of the model and achieve efficient leaf-wood separation. The proposed LWSNet is tested on eight species of trees with different characteristics and sizes. The average F1 score for leaf-wood separation is as high as 97.29%. The results show that this method outperforms the state-of-the-art leaf-wood separation methods in previous studies, and can accurately and robustly separate leaves and wood in trees of different species, sizes, and structures. This study extends the leaf-wood separation of tree point clouds in an end-to-end manner and demonstrates that the deep-learning segmentation algorithm has a great potential for processing tree and plant point clouds with complex morphological traits.
Assessment of Urban Forest Ecological Benefit Based on the i-Tree Eco Model—A Case Study of Changchun Central City
Authors: Zhao Hongyu , Zhao Dongliang , Jiang Xue , Zhang Shiyu , Lin Zhanlue
Published: June 2023

Urban forests are one of the most ecologically significant systems in urban ecosystems. To make the layout and input–output ratio of urban forests more economically rational for sustainable strategic planning, it is necessary to assess the ecological benefits and ecosystem services of urban forests according to the local geographical characteristics of different cities and analyse their cost–benefit relationships. In this study, the i-Tree Eco model was used to assess the ecological benefits of urban forests in terms of four aspects: carbon sequestration and oxygen release, energy saving, rainwater retention, and air quality improvement. To translate them into economic benefits, using mathematical and statistical analysis, the cost–benefit relationship of urban forests with different tree and shrub proportions was analysed, and the impact range of urban forests with different layout types was compared. The research found that: (1) tree species are the main influencing factor of urban forest ecological benefits, (2) linear urban forests have a wider impact range, (3) if the proportion of trees in urban forests in the research area is adjusted to 0.36, the ecological benefits can increase by RMB 0.061 billion per year. We provide efficient and convenient research paths and tools for studying the cost–benefit relationship. By using an i-Tree Eco model, we realized the economic characteristics of urban forests. This research provides quantitative support for the balanced construction of urban ecological civilization and economic benefits. It can provide quantitative support for a balance between urban ecological development, economic development, and spatial optimization.
Effect of Litter Removal and Addition on Root Exudation and Associated Microbial N Transformation in a Pinus massoniana Plantation
Authors: Zhang Chengfu , Zhao Qingxia , Cai Yinmei , Zhang Tao , Zhang Limin , He Tengbing
Published: June 2023

In forest ecosystems, variations in aboveground litter input caused by global changes, substantially alter soil N cycling. In field-grown plants, few studies have directly measured root exudation rates and quantified their effects on N transformations under litter manipulation. We quantified soil N transformation rate responses to litter manipulation in a Pinus massoniana plantation, and unravelled the effect of root exudation on soil N transformations. We measured in situ P. massoniana root exudation rates as well as soil microbial biomass, soil C and N concentrations, the activities of four soil enzymes involved in soil N transformations, and net N mineralization and net nitrification rates after experimental litter removal and litter addition treatments. Litter removal and litter addition treatments had little impact on soil C and N concentrations, microbial biomass, soil enzyme (urease, hydroxylamine reductase, nitrate reductase, and nitrite reductase) activity, and net N mineralization rates. However, both litter removal and addition increased net N nitrification rates. Additionally, litter removal significantly decreased root C exudation rates (in April 2021 and annually), whereas litter addition had no significant effects on root C exudation rates across all seasons. Furthermore, root C exudation rates were positively associated with urease and nitrate reductase activities, but negatively associated with hydroxylamine reductase and nitrite reductase activities, as well as net N nitrification rate. Overall, we demonstrated that root exudates may be an important physiological adjustment by which trees respond to changes in litter input caused by global environmental changes, regulating underground N biochemical processes. Furthermore, we provide new evidence from root exudates for understanding the potential influence of litter inputs on soil N cycling. A strong correlation exists between root exudates and N transformation, shedding new light on the dynamics of rhizosphere nutrient cycling crucial for maintaining forest ecosystem stability and productivity under changing environmental conditions.
Patterns and Driving Mechanism of C, N, P Ecological Stoichiometry in Plant-Litter-Soil Systems of Monoculture and Mixed Coastal Forests in Southern Zhejiang Province of China
Authors: Bao Binghui , Huang Xiaoling , Xu Haidong , Xie Hongtao , Cheng Xiangrong
Published: June 2023

Mixed forests are usually associated with higher resource utilization compared to the corresponding monocultures; however, the tree mixing effects of carbon (C), nitrogen (N), phosphorus (P) ecological stoichiometry in coastal forest ecosystems remains largely unknown. We compared the C, N, P stoichiometry in different ecosystem components (i.e., canopy layer, herb layer, litter layer, 0–20 cm and 20–40 cm soils) among two monocultures (Casuarina equisetifolia and Eucalyptus saligna) and their mixture in Taizhou, Zhejiang province, China. We also assessed the effects of the main microhabitat factors (wind speed, soil salinity, soil moisture and pH) on C, N, P stoichiometry. Two monocultures and their mixture showed the same elemental pattern of “low C and high P” for both the canopy and herb layers, and soil, indicating evident N limitations; however, the mixture intensified the N deficiency more. The mixture showed stronger correlations among the C, N, P stoichiometry than the monocultures. Redundancy and hierarchical partitioning analysis showed the overall and independent effects of the microhabitat factors on the C, N, P stoichiometry separately, in which soil moisture presented more effects on shallow soil (20–40 cm) C, N, and P, while soil salinity mainly affected the herb and litter layers; wind speed had greater effects on canopy layer C, N, P stoichiometry. These results are expected to provide a management reference for the regeneration of degraded plantations in the southern Zhejiang province of China.
The Production of Bioaroma by Auriporia aurulenta Using Agroindustrial Waste as a Substrate in Submerged Cultures
Authors: Sandes Rafael Donizete Dutra , De Jesus Mônica Silva , Araujo Hannah Caroline Santos , Dos Santos Raquel Anne Ribeiro , Nogueira Juliete Pedreira , Leite Neta Maria Terezinha Santos , Narain Narendra
Published: June 2023

The present study was carried out to investigate the potential of the basidiomycete Auriporia aurulenta to metabolize residues remaining from the processing of umbu, cajá, plum, and persimmon fruits for the production of natural aroma compounds using submerged fermentation. The volatile compounds obtained from the fermentation of A. aurulenta cultivated in these residues were extracted via stir bar sorptive extraction (SBSE) and analyzed using a gas chromatography-mass spectrometry (GC-MS) system. Esters and alcohols were the main compounds produced, with emphasis on the compounds 2-phenethyl acetate and 2-phenylethanol, which were mainly produced from umbu residue. The acid medium favored the production of 2-phenethyl acetate, reaching its maximum value (11.38 mg/L) on day 3.5, while higher concentrations of 2-phenylethanol were found in the basic medium, with optimal production (2.27 mg/L) on the 7th day. By varying the concentrations of pre-inoculum and residue in the optimization of this fermentation process, it was possible to double the production (24.47 mg/L) of 2-phenethyl acetate and obtain a seven times higher concentration (15.56 mg/L) of 2-phenylethanol. The diversity and expressive production of these aromatic compounds found in the fermentation media using these agroindustrial residues indicate that their use as substrates is an economical and environmentally viable alternative.
An Ontology for Spatio-Temporal Media Management and an Interactive Application
Authors: Sone Takuro , Kato Shin , Atarashi Ray , Nakazato Jin , Tsukada Manabu , Esaki Hiroshi
Published: June 2023

In addition to traditional viewing media, metadata that record the physical space from multiple perspectives will become extremely important in realizing interactive applications such as Virtual Reality (VR) and Augmented Reality (AR). This paper proposes the Software Defined Media (SDM) Ontology designed to describe spatio-temporal media and the systems that handle them comprehensively. Spatio-temporal media refers to video, audio, and various sensor values recorded together with time and location information. The SDM Ontology can flexibly and precisely represent spatio-temporal media, equipment, and functions that record, process, edit, and play them, as well as related semantic information. In addition, we recorded classical and jazz concerts using many video cameras and audio microphones, and then processed and edited the video and audio data with related metadata. Then, we created a dataset using the SDM Ontology and published it as linked open data (LOD). Furthermore, we developed “Web3602”, an application that enables users to interactively view and experience 360∘ video and spatial acoustic sounds by referring to this dataset. We conducted a subjective evaluation by using a user questionnaire. Web3602 is a data-driven web application that obtains video and audio data and related metadata by querying the dataset.
ID2S4FH: A Novel Framework of Intelligent Decision Support System for Fire Hazards
Authors: Kumar Kanak , Rajput Navin Singh , Shvetsov Alexey V. , Saif Abdu , Sahal Radhya , Alsamhi Saeed Hamood
Published: June 2023

Modern societies and industrial sectors are serviced through storage and distribution centres (SDCs) such as supermarkets, malls, warehouses, etc. Large quantities of supplies are stocked here, e.g., food grains, clothes, shoes, pharmaceuticals, electronics, plastics, edible oils, electrical wires/equipment, petroleum products, painting materials, etc. Fires due to the burning of these materials are categorized into six classes, viz., Class A, Class B, Class C, Class D, Class K, and Class F. A fire is extinguished better when the right type of fire retardant is used. A thumb rule on firefighting also says, “never fight a fire if you do not know what is burning”. In this paper, we have proposed an Intelligent Decision Support System (ID2S4FH) to generate a real-time ‘fire-map’ of such SDCs during a fire hazard. We have interfaced six tin-oxide-based gas sensor elements, a temperature and humidity sensor, and a particulate matter (PM) sensor with microcontrollers to capture the real-time signature patterns of the ambient air. We burned sixteen different types of materials belonging to six classes of fire and created a dataset consisting of 2400 samples. The sensor array responses were then pre-processed and analysed using various classifiers trained in different analysis space domains. Among the classifiers, four classifiers achieved ‘all correct’ identification of the fire classes of 80 unknown test samples, and the lowest mean squared error (MSE) achieved was 2.81 × 10−3. During a fire hazard, our proposed ID2S4FH can generate real-time fire maps of SDCs and help firefighters to extinguish the fire using the appropriate fire retardant.
Thermal Effects on Ecological Traits of Salmonids
Authors: Jonsson Bror
Published: June 2023

Here, I review thermal influences on metabolic rates and aerobic scope; growth; adult body size; and reproductive and behavioural traits, such as tendency and timing of the migration of salmonid fishes. A thermal window bounded by the upper and lower incipient lethal temperatures (UILT and LILT) determines where salmonids can survive. For most salmonids, LILT is close to 0 and UILT is between 20 and 30 °C. UILT and LILT are influenced by the acclimation temperature. Thermal tolerance is affected by fish size and ambient oxygen content, which decreases with increasing temperature. Standard metabolic rate (SMR), the energy required to maintain essential functions, increases with temperature, whereas maximum metabolic rate (MMR) increases with temperature until reaching a peak (pejus). Then, it decreases gradually to zero, i.e., the upper critical limit (TCrit). Aerobic scope (AS = MMR-SMR) reaches its maximum at the pejus temperature. Metabolic rates and aerobic scope can be modified by temperatures that the fish experiences during embryogenesis and possibly also as larvae and young fry. At maximum feeding, maximum growth increases to a point at or below the pejus temperature. The optimum temperature for growth decreases with reduced food intake and increased body size. As for metabolic rate, the growth rate is influenced by the temperature during embryonic development. In a warmer climate, adult body size is expected to decrease chiefly because of a younger age at maturity. Parental fish retained at a higher temperature during maturation produce larger eggs, and this change in egg size may also be transferred to next-generation offspring. Furthermore, embryogenesis in warmer water leads to larger gonad and egg sizes at maturity. Water temperature influences locomotion, foraging and migratory activity. In a warmer climate, juveniles migrate to the sea earlier in spring. In addition, higher embryo temperature leads to delayed return of adult salmon from the ocean. Thus, temperature affects life history traits of salmonid fishes, partly as a direct effect on metabolic rates and food consumption and partly induced as a phenotypically plastic effect. The phenotypically plastic response may preadapt offspring to perform better in the expected future thermal environment.
Upregulation of Heat-Shock Protein (hsp)-27 in a Patient with Heterozygous SPG11 c.1951C>T and SYNJ1 c.2614G>T Mutations Causing Clinical Spastic Paraplegia
Authors: García-Carmona Juan , Amores-Iniesta Joaquín , Soler-Usero José , Cerdán-Sánchez María , Navarro-Zaragoza Javier , López-López María , Soria-Torrecillas Juan , Ballesteros-Arenas Ainhoa , Pérez-Vicente José , Almela Pilar
Published: June 2023

We report a 49-year-old patient suffering from spastic paraplegia with a novel heterozygous mutation and analyzed the levels of heat shock proteins (hsp)-27, dopamine (DA), and its metabolites in their cerebrospinal fluid (CSF). The hsp27 protein concentration in the patient’s CSF was assayed by an ELISA kit, while DA levels and its metabolites in the CSF, 3,4-dihydroxyphenylacetic acid (DOPAC), Cys-DA, and Cys-DOPA were measured by HPLC. Whole exome sequencing demonstrated SPG-11 c.1951C>T and novel SYNJ1 c.2614G>T mutations, both heterozygous recessive. The patient’s DA and DOPAC levels in their CSF were significantly decreased (53.0 ± 6.92 and 473.3 ± 72.19, p < 0.05, respectively) while no differences were found in their Cys-DA. Nonetheless, Cys-DA/DOPAC ratio (0.213 ± 0.024, p < 0.05) and hsp27 levels (1073.0 ± 136.4, p < 0.05) were significantly higher. To the best of our knowledge, the c.2614G>T SYNJ1 mutation has not been previously reported. Our patient does not produce fully functional spatacsin and synaptojanin-1 proteins. In this line, our results showed decreased DA and DOPAC levels in the patient’s CSF, indicating loss of DAergic neurons. Many factors have been described as being responsible for the increased cys-DA/DOPAC ratio, such as MAO inhibition and decreased antioxidant activity in DAergic neurons which would increase catecholquinones and consequently cysteinyl-catechols. In conclusion, haploinsufficiency of spatacsin and synaptojanin-1 proteins might be the underlying cause of neurodegeneration produced by protein trafficking defects, DA vesicle trafficking/recycling processes, autophagy dysfunction, and cell death leading to hsp27 upregulation as a cellular mechanism of protection and/or to balance impaired protein trafficking.
Genetic Diversity of Common Olive (Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method
Authors: Slobodova Natalia , Sharko Fedor , Gladysheva-Azgari Maria , Petrova Kristina , Tsiupka Sergey , Tsiupka Valentina , Boulygina Eugenia , Rastorguev Sergey , Tsygankova Svetlana
Published: June 2023

In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection of common olive’s cultivars and hybrids has been collected in the Nikitsky Botanical Gardens (NBG). The aim of this study was to assess the genetic diversity of 151 samples (total of several biological replicates of 46 olive cultivars including 29 introduced and 11 indigenous genotypes) using the ddRAD sequencing method. Structural analysis showed that the studied samples are divided into ten groups, each of which mainly includes cultivars of the same origin. Cultivars introduced to the Crimean Peninsula from different regions formed separate groups, while local cultivars joined different groups depending on their origin. Cultivars of Crimean origin contain admixtures of mainly Italian and Caucasian cultivars’ genotypes. Our study showed that the significant number of Crimean cultivars contains an admixture of the Italian cultivar “Coreggiolo”. Genetic analysis confirmed the synonymy for the cv. “Otur” and “Nikitskaya 2”, but not for the other four putative synonyms. Our results revealed the genetic diversity of the olive collection of NBG and provided references for future research studies, especially in selection studies for breeding programs.
Female Pattern Hair Loss: An Overview with Focus on the Genetics
Authors: Ho Chih-Yi , Chen Jeff Yi-Fu , Hsu Wen-Li , Yu Sebastian , Chen Wei-Chiao , Chiu Szu-Hao , Yang Hui-Ru , Lin Sheng-Yao , Wu Ching-Ying
Published: June 2023

Pattern hair loss can occur in both men and women, and the underlying molecular mechanisms have been continuously studied in recent years. Male androgenetic alopecia (M-AGA), also termed male pattern hair loss, is the most common type of hair loss in men. M-AGA is considered an androgen-dependent trait with a background of genetic predisposition. The interplay between genetic and non-genetic factors leads to the phenotype of follicular miniaturization. Although this similar pattern of phenotypic miniaturization can also be found in female pattern hair loss (FPHL), the corresponding genetic factors in M-AGA do not account for the phenotype in FPHL, indicating that there are different genes contributing to FPHL. Therefore, the role of genetic factors in FPHL is still uncertain. Understanding the genetic mechanism that causes FPHL is crucial for the future development of personalized treatment strategies. This review aims to highlight the differences in the ethnic prevalence and genetic background of FPHL, as well as the current genetic research progress in nutrition, Wnt signaling, and sex hormones related to FPHL.
Cloning and Functional Verification of Endogenous U6 Promoters for the Establishment of Efficient CRISPR/Cas9-Based Genome Editing in Castor (Ricinus communis)
Authors: Kanai Masatake , Hikino Kazumi , Mano Shoji
Published: June 2023

Castor (Ricinus communis) seeds are rich in a type of hydroxy fatty acid called ricinoleic acid, which is in high demand for the production of plant-based plastics, lubricants, and hydraulic oils. However, the high content of ricin, a toxic protein, in these seeds has restricted further expansion in the area of castor cultivation. Therefore, the development of ricin-free castor is needed. Genome editing technology, although successfully applied in several plant species, is still in the developing stages in castor and awaits the identification of an endogenous U6 promoter with robust function. Here, we searched for U6 small nuclear RNA (snRNA) genes in the castor genome. This led to the identification of six U6 snRNA genes. The promoters of these U6 snRNA genes were cloned, and their function was examined in castor cells using the particle delivery method. The results showed that a U6 promoter length of approximately 300 bp from the transcription start site was sufficient to activate gene expression. This study provides insights into the endogenous castor U6 promoter sequences and outlines a method for verifying the function of U6 promoters in plants using the particle delivery system.
The APOBEC3B c.783delG Truncating Mutation Is Not Associated with an Increased Risk of Breast Cancer in the Polish Population
Authors: Gliniewicz Katarzyna , Kluźniak Wojciech , Wokołorczyk Dominika , Huzarski Tomasz , Stempa Klaudia , Rudnicka Helena , Jakubowska Anna , Szwiec Marek , Jarkiewicz-Tretyn Joanna , Naczk Mariusz , Kluz Tomasz , Dębniak Tadeusz , Gronwald Jacek , Lubiński Jan , Narod Steven A. , Akbari Mohammad R. , Cybulski Cezary
Published: June 2023

The APOBEC3B gene belongs to a cluster of DNA-editing enzymes on chromosome 22 and encodes an activation-induced cytidine deaminase. A large deletion of APOBEC3B was associated with increased breast cancer risk, but the evidence is inconclusive. To investigate whether or not APOBEC3B is a breast cancer susceptibility gene, we sequenced this gene in 617 Polish patients with hereditary breast cancer. We detected a single recurrent truncating mutation (c.783delG, p.Val262Phefs) in four of the 617 (0.65%) hereditary cases by sequencing. We then genotyped an additional 12,484 women with unselected breast cancer and 3740 cancer-free women for the c.783delG mutation. The APOBEC3B c.783delG allele was detected in 60 (0.48%) unselected cases and 19 (0.51%) controls (OR = 0.95, 95% CI 0.56–1.59, p = 0.94). The allele was present in 8 of 1968 (0.41%) familial breast cancer patients from unselected cases (OR = 0.80, 95% CI 0.35–1.83, p = 0.74). Clinical characteristics of breast tumors in carriers of the APOBEC3B mutation and non-carriers were similar. No cancer type was more frequent in the relatives of mutation carriers than in those of non-carriers. We conclude the APOBEC3B deleterious mutation p.Val262Phefs does not confer breast cancer risk. These data do not support the hypothesis that APOBEC3B is a breast cancer susceptibility gene.
ICAnnoLncRNA: A Snakemake Pipeline for a Long Non-Coding-RNA Search and Annotation in Transcriptomic Sequences
Authors: Pronozin Artem Yu. , Afonnikov Dmitry A.
Published: June 2023

Long non-coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not encode proteins. Experimental studies have shown the diversity and importance of lncRNA functions in plants. To expand knowledge about lncRNAs in other species, computational pipelines that allow for standardised data-processing steps in a mode that does not require user control up until the final result were actively developed recently. These advancements enable wider functionality for lncRNA data identification and analysis. In the present work, we propose the ICAnnoLncRNA pipeline for the automatic identification, classification and annotation of plant lncRNAs in assembled transcriptomic sequences. It uses the LncFinder software for the identification of lncRNAs and allows the adjustment of recognition parameters using genomic data for which lncRNA annotation is available. The pipeline allows the prediction of lncRNA candidates, alignment of lncRNA sequences to the reference genome, filtering of erroneous/noise transcripts and probable transposable elements, lncRNA classification by genome location, comparison with sequences from external databases and analysis of lncRNA structural features and expression. We used transcriptomic sequences from 15 maize libraries assembled by Trinity and Hisat2/StringTie to demonstrate the application of the ICAnnoLncRNA pipeline.
A Case of Class I 17p13.3 Microduplication Syndrome with Unilateral Hearing Loss
Authors: Vittas Spiros , Bisba Maria , Christopoulou Georgia , Apostolakopoulou Loukia , Pons Roser , Constantoulakis Pantelis
Published: June 2023

17p13 is a chromosomal region characterized by genomic instability due to high gene density leading to multiple deletion and duplication events. 17p13.3 microduplication syndrome is a rare condition, reported only in 40 cases worldwide, which is found in the Miller–Dieker chromosomal region, presenting a wide range of phenotypic manifestations. Usually, the duplicated area is de novo and varies in size from 1.8 to 4.0 Mbp. Critical genes for this region are PAFAH1B1 (#601545), YWHAE (#605066), and CRK (#164762). 17p13.3 microduplication syndrome can be categorized into two classes (Class I and Class II) based on the genes that are present in the duplicated area, which lead to different phenotypes. In this report, we present a new case of Class I 17p13.3 microduplication syndrome that presents with unilateral sensorineural hearing loss. Oligonucleotide and SNP array comparative genomic hybridization (a-CGH) analysis revealed a duplication of approximately 121 Kbp on chromosome 17p13.3, which includes YWHAE and CRK genes. Whole-exome sequencing (WES) analysis confirmed the duplication. Our patient has common clinical symptoms of Class I 17p13.3 microduplication syndrome, and in addition, she has unilateral sensorineural hearing loss. Interestingly, WES analysis did not detect any mutations in genes that are associated with hearing loss. The above findings lead us to propose that hearing loss is a manifestation of 17p13.3 duplication syndrome.
Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats
Authors: Zou Yue , Chen Xiang , Tian Xingzhou , Guo Wei , Ruan Yong , Tang Wen , Fu Kaibin , Ji Taotao
Published: June 2023

Reproductive competence in male mammals depends on testicular function. Testicular development and spermatogenesis in goats involve highly complex physiological processes. In this study, six testes were, respectively, obtained from each age group, immature (1 month), sexually mature (6 months) and physically mature (12 months old) Qianbei Ma goats. RNA-Seq was performed to assess testicular mRNA expression in Qianbei Ma goats at different developmental stages. Totally, 18 libraries were constructed to screen genes and pathways involved in testis development and spermatogenesis. Totally, 9724 upregulated and 4153 downregulated DEGs were found between immature (I) and sexually mature (S) samples; 7 upregulated and 3 downregulated DEGs were found between sexually mature (S) and physically mature (P) samples, and about 4% of the DEGs underwent alternative splicing events between I and S. Select genes were assessed by qRT-PCR, corroborating RNA-Seq findings. The detected genes have key roles in multiple developmental stages of goat testicular development and spermatogenesis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine differentially expressed genes (DEGs). GO analysis revealed DEGs between S and P contributed to “reproduction process”, “channel activity” and “cell periphery part” between I and S, and in “ion transport process”, “channel activity” and “transporter complex part”. KEGG analysis suggested the involvement of “glycerolipid metabolism”, “steroid hormone biosynthesis” and “MAPK signaling pathway” in testis development and spermatogenesis. Genes including IGF1, TGFB1, TGFBR1 and EGFR may control the development of the testis from immature to sexually mature, which might be important candidate genes for the development of goat testis. The current study provides novel insights into goat testicular development and spermatogenesis.
Antagonistic Bacteria Bacillus velezensis VB7 Possess Nematicidal Action and Induce an Immune Response to Suppress the Infection of Root-Knot Nematode (RKN) in Tomato
Authors: Kamalanathan Vinothini , Sevugapperumal Nakkeeran , Nallusamy Saranya
Published: June 2023

Meloidogyne incognita, the root-knot nematode (RKN), a devastating plant parasitic nematode, causes considerable damage to agricultural crops worldwide. As a sedentary root parasite, it alters the root’s physiology and influences the host’s phytohormonal signaling to evade defense. The sustainable management of RKN remains a challenging task. Hence, we made an attempt to investigate the nematicide activity of Bacillus velezensis VB7 to trigger the innate immune response against the infection of RKN. In vitro assay, B. velezensis VB7 inhibited the hatchability of root-knot nematode eggs and juvenile mortality of M. incognita by 87.95% and 96.66%, respectively at 96 hrs. The application of B. velezensis VB7 challenged against RKN induced MAMP-triggered immunity via the expression of transcription factors/defense genes by several folds pertaining to WRKY, LOX, PAL, MYB, and PR in comparison to those RKN-inoculated and healthy control through RT-PCR. Additionally, Cytoscape analysis of defense genes indicated the coordinated expression of various other genes linked to immune response. Thus, the current study clearly demonstrated the effectiveness of B. velezensis VB7 as a potential nematicide and inducer of immune responses against RKN infestation in tomato.
Effects of Salinity Stress on Growth and Physiological Parameters and Related Gene Expression in Different Ecotypes of Sesuvium portulacastrum on Hainan Island
Authors: Wang Yong , Ma Wei , Fu Haijiang , Li Liting , Ruan Xueyu , Zhang Xueyan
Published: June 2023

We conducted a study to examine the growth and physiological changes in 12 different ecotypes of Sesuvium portulacastrum collected from Hainan Island in China. These ecotypes were subjected to different concentrations (0, 200, 400, and 600 mmol/L) of sodium chloride (NaCl) salt stress for 14 days. We also analyzed the expression of metabolic genes related to stress response. Under low salt stress, indicators such as plant height in region K (0 mmol/L: 45% and highest at 200 mmol/L: 80%), internode length (0 mmol/L: 0.38, 200 mmol/L: 0.87, 400 mmol/L: 0.25, and 600 mmol/L: 1.35), as well as leaf area, relative water content, fresh weight, and dry weight exhibited an overall increasing trend with the increase in salt concentration. However, as the salt concentration increased, these indicators showed a decreasing trend. Proline and malondialdehyde contents increased with higher salt concentrations. When the NaCl concentration was 400 mmol/L, MDA content in the leaves was highest in the regions E (196.23%), F (94.28%), J (170.10%), and K (136.08%) as compared to the control group, respectively. Most materials demonstrated a significant decrease in chlorophyll a, chlorophyll b, and total chlorophyll content compared to the control group. Furthermore, the ratio of chlorophyll a to chlorophyll b (Rab) varied among different materials. Using principal component analysis, we identified three ecotypes (L from Xinglong Village, Danzhou City; B from Shuigoupo Village, Lingshui County; and J from Haidongfang Park, Dongfang City) that represented high, medium, and low salt tolerance levels, respectively, based on the above growth and physiological indexes. To further investigate the expression changes of related genes at the transcriptional level, we employed qRT-PCR. The results showed that the relative expression of SpP5CS1, SpLOX1, and SpLOX1 genes increased with higher salt concentrations, which corresponded to the accumulation of proline and malondialdehyde content, respectively. However, the relative expression of SpCHL1a and SpCHL1b did not exhibit a consistent pattern. This study contributes to our understanding of the salt tolerance mechanism in the true halophyte S. portulacastrum, providing a solid theoretical foundation for further research in this field.
The Impact of the Historical–Architectural Component on Property Value
Authors: Manganelli Benedetto , Tajani Francesco , De Paola Pierfrancesco , Del Giudice Francesco Paolo
Published: June 2023

The historic designation of individual properties and entire neighborhoods has experienced an evolution in its meaning in recent decades. The original passive approach to managing historical buildings, which primarily regarded them as “values” to be defended and preserved for future generations, has been supplemented by strategies aimed at their valorization, derived from an awareness of the potential of such resources for the community, as a means of promoting the economic and social conditions of local populations. This paper proposes a review of all the main research carried out in the literature over the last thirty years concerning the impact of the historical–architectural significance of property values, both from an intrinsic point of view by evaluating the weight that the examined variable assumes in relation to the market value of the individual property and an extrinsic point of view by addressing the issue of the evaluation of “spatial spillovers”, positive and/or negative externalities that neighborhoods with historical–architectural significance—understood as historical districts—produce on the values of the properties falling within them. The analysis conducted shows that, according to the studies carried out, historic-architectural value can have both a positive and negative impact on property values. This output is related to the type of historic designation (local rather than national), the architectural style, the building typology, and the conservation and enhancement activities envisaged for the property.
Research Progress on the Medicinal and Edible Polygala fallax Hemsl. (Polygalaceae) Plant
Authors: Wu Chao , Zhang Xiujiao , Liu Baoyu , Tang Hui
Published: June 2023

Polygala fallax Hemsl., a species belonging to the genus Polygala and the family Polygalaceae, is primarily distributed in southern China. Wild P. fallax Hemsl. (Polygalaceae) is currently endangered, but its utilization value has not yet been thoroughly investigated. The present review summarizes the morphological and structural characteristics, wild resource distribution, chemical constituents and pharmacological efficacy, artificial breeding and cultivation techniques, and utilization value of P. fallax Hemsl. (Polygalaceae) to facilitate future studies on the conservation and use of P. fallax Hemsl plants. We conclude that (i) P. fallax Hemsl. (Polygalaceae) is a medicinal and edible plant, and also has eco-economic and ornamental value; (ii) roots are the primary medicinal parts, which contain pharmacologically active compounds such as saponins, flavones, oligosaccharide polyesters, polysaccharides, sterols, organic acids, etc.; and (iii) P. fallax Hemsl. (Polygalaceae) shows various pharmacological efficacies including anti-inflammatory effects, antivirus effects, antioxidative effects, an immunity-boosting function, hepatic-protective effects, hypolipidemic effect, blood-activating, stasis-eliminating effects, and antitumor, etc. More research on the applications of P. fallax Hemsl. (Polygalaceae) are needed, especially efforts to identify its effective constituents, pharmacological efficacy, quality control, and clinical applications. The use of P. fallax Hemsl. (Polygalaceae) resources should be enhanced, especially the use of the aboveground parts, and the pharmacological efficacy of other chemical constituents, such as flavones and polysaccharides, should be further explored.
Enhancing the Growth Performance, Cellular Structure, and Rubisco Gene Expression of Cadmium Treated Brassica chinensis Using Sargassum polycystum and Spirulina platensis Extracts
Authors: Shaari Nurul Elyni Mat , Khandaker Mohammad Moneruzzaman , Tajudin Md. Tajol Faeiz Md. , Majrashi Ali , Alenazi Mekhled Mutiran , Badaluddin Noor Afiza , Adnan Ahmad Faris Mohd , Osman Normaniza , Mohd Khamsah Suryati
Published: June 2023

Cadmium (Cd) is one of the highly toxic, non-essential heavy metals that inhibit plant growth and development by prompting chlorophyll loss and affecting photosynthetic activities. This study investigated the efficacy of Spirulina platensis and Sargassum polycystum extracts in alleviating Cd stress in Pak Choi at morpho-biochemical, anatomical, and molecular levels. Different concentrations (0, 25, 50, and 100 mL/L) of S. polycyctum (SAR), S. platensis (SPI), and a mixture of both extracts (SS) were exposed to 100 mg/kg Cd-contaminated Pak Choi seedlings. Non-Cd-treated Pak Choi and Cd-contaminated Pak Choi without algal extracts were assigned as positive and negative controls, respectively. The results showed that the application of algal extracts increased the plant height, fresh weight (FW), and dry weight (DW) as the extract level increased. This was greatest in 100SS with 37.51% (shoot length), 68.91% (root length), 110.8% (shoot DW), and 216.13% (root DW), while an increase of 176.7% (shoot FW) and 256.9% (root FW) was seen in the 100SPI treatment. Chlorophyll a, b, carotenoid, and chlorophyll fluorescence increased significantly after the treatment with 100SS. Antioxidant enzymes CAT, APX, POD, and protein were significantly increased in 100 mL/L extracts by 28.13% (100SS), 36.40% (100SAR), 46.92% (100SS), and 153.48% (100SS), respectively. The same treatment was also identified to dominate the development of root structures such as total length, surface area, projected area, diameter, volume, tips, and fork number. The highest reduction of Cd content in the root and shoot of Pak Choi was observed in 100SS with a 53.8% and 39.88% decrease, respectively. Increasing algal extract concentration also improved the leaf histological characteristics substantially, such as stomatal size and opening, mesophyll tissues, and vascular bundles. In addition, the fold change ratio of the Rubisco gene at 100SS treatment was noticeably greater than other algal extract treatments, with a 0.99 fold change when compared with the untreated sample. This present study illustrated that Sargassum polycyctum and Spirulina platensis extracts have the potential to effectively alleviate Cd stress in Pak Choi plants, especially with the application of 100 mL/L of an algal extract mixture. These findings contribute to the development of sustainable strategies for mitigating Cd toxicity in crops.
Genetic Diversity and Population Structure Analysis of Anatolian Kara Grapevine (Vitis vinifera L.) Germplasm Using Simple Sequence Repeats
Authors: Arslan Nur , Yılmaz Baydu Funda , Hazrati Nahid , Yüksel Özmen Canan , Ergönül Onur , Uysal Tamer , Yaşasın Ahmet Semih , Özer Cengiz , Boz Yılmaz , Kuleyin Yusuf Serhat , Ergül Ali
Published: June 2023

Grape (Vitis vinifera L.) is among the most important commercial fruit species grown worldwide in terms of its economic value. Anatolia (Turkey), located in the favorable climate zone for viticulture, has a rich grape genetic potential due to its location at the intersection of the grapevine gene centers. In Turkish Kara grape germplasm, there are problems in terms of accuracy during the production phase due to the inadequacies in ampelographic definitions, and also very little information is available on genetic analysis of Kara grape germplasm. This study carried out genetic analysis of 49 Kara grape cultivars from six regions (sub-populations) of Turkey and 3 reference cultivars using 22 microsatellite loci (SSR), and ampelographic analysis were also performed concerning 39 OIV descriptors. In the SSR analysis, the average number of alleles per locus was 8.91, ranging from 4 to 13; four synonymous and five homonymous cases were also identified. In the population structure analysis, the genetic differentiation (Fst) values among six populations were moderate. In the BAPS analysis, all populations except Central Anatolia were found to be highly admixed with each other, and in the FCA analysis, the East Anatolia population was completely separated. In the multilocus lineages (MLLs) analysis, a total of three accessions were matched to different accessions as clone assignment. In this study, SSR-based genetic characterization of the Turkish Kara grape germplasm was revealed for the first time, and it is thought that the obtained data will help other grape genetic characterization studies and contribute to viticulture research in other areas such as breeding, protection and variety registration.