Search Results (142)

Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance. Full article

Interferon (IFN) signaling plays vital roles in host defense against viral infection. However, a variety of observations have been reported in the literature regarding the roles of IFN signaling in COVID-19. Thus, it would be important to reach a clearer picture regarding the activation or suppression of IFN signaling in COVID-19. In this work, regulation of marker genes for IFN signaling was examined in natural infection, viral challenge, and vaccination based on 13 public transcriptome datasets. Three subsets of interferon-stimulated genes (ISGs) were selected for detailed examination, including one set of marker genes for type I IFN signaling (ISGa) and two sets of marker genes for type II IFN signaling (IFN-γ signaling, GBPs for the GBP gene cluster, and HLAd for the HLA-D gene cluster). In natural infection, activation of ISGa and GBPs was accompanied by the suppression of HLAd in hospitalized patients. Suppression of GBPs was also observed in certain critical conditions. The scale of regulation was much greater for ISGa than that of GBPs and HLAd. In addition, the suppression of HLAd was correlated with disease severity, and it took much longer for HLAd to return to the level of healthy controls than that for ISGa and GBPs. Upon viral challenge, the activation of ISGa and GBPs was similar to that of natural infection, while the suppression of HLAd was not observed. Moreover, GBPs’ return to the pre-infection level was at a faster pace than that of ISGa. Upon COVID-19 vaccination, activation was observed for all of these three gene sets, and the scale of activation was comparable for ISGa and GBPs. Notably, it took a much shorter time for GBPs and ISGa to return to the level of healthy controls than that in COVID-19 infection. In addition, the baseline values and transient activation of these gene sets were also associated with subsequent vaccination response. The intricate balance of IFN signaling was demonstrated in mild breakthrough infection, where attenuated response was observed in people with prior vaccination compared to that in vaccine-naïve subjects. Overall, distinctive temporal profiles of IFN signaling were observed in natural infection, viral challenge, and vaccination. The features observed in this work may provide novel insights into the disease management and vaccine development. Full article

The use of chloride-based deicing salts, particularly sodium chloride (NaCl) and calcium chloride (CaCl₂), is a common practice in cold regions for maintaining road safety during winter. However, the accumulation of salt residues in adjacent soils poses serious environmental threats, including reduced pH, increased electrical conductivity (EC), disrupted soil structure, and plant growth inhibition. This study aimed to evaluate the combined effect of activated carbon (AC) and Pennisetum alopecuroides, a salt-tolerant perennial grass, in alleviating salinity stress under deicer-treated soils. A factorial greenhouse experiment was conducted using three fixed factors: (i) presence or absence of Pennisetum alopecuroides, (ii) deicer type (NaCl or CaCl₂), and (iii) activated carbon mixing ratio (0, 1, 2, 5, and 10%). Soil pH, EC, and ion concentrations (Na⁺, Cl⁻, Ca²⁺) were measured, along with six plant growth indicators. The results showed that increasing AC concentrations significantly increased pH and reduced EC and ion accumulation, with the 5% AC treatment being optimal in both deicer systems. Plant physiological responses were improved in AC-amended soils, especially under CaCl₂ treatment, indicating less ion toxicity and better root zone conditions. The interaction effects between AC, deicer type, and plant presence were statistically significant (p < 0.05), supporting a synergistic remediation mechanism involving both adsorption and biological uptake. Despite the limitations of short-term controlled conditions, this study offers a promising phytomanagement strategy using natural adsorbents and salt-tolerant plants for sustainable remediation of salt-affected soils in road-adjacent and urban environments. Full article

Light-harvesting chlorophyll a/b-binding (Lhc) proteins are integral membrane proteins that bind to pigment molecules, playing a critical role in photosynthetic processes, including light energy harvesting and transfer. To investigate the role of the Lhc gene family in cucumber (Cucumis sativus L), genome-wide identification of CsLhc gene family members and analysis of their regulatory networks were carried out using bioinformation and molecular biology research methods at Anhui Science and Technology University. The results indicated that the Lhc family consisted of 21 members, being categorized into five subfamilies: Lhca, Lhcb, CP24, CP26, and CP29. The gene structure and motifs within each subfamily are generally conserved. CsLhcs are distributed on seven chromosomes, including one pair of tandem duplicates and two pairs of segmental duplicates. Six CsLhcs exhibit eight linear relationships with seven AtLhcs, and one CsLhc shows a syntenic relationship with one OsLhc. Analysis of the cis-acting elements in CsLhc promoters revealed their potential involvement in stress responses. Transcriptome data indicated that CsLhcs are minimally expressed in male flowers and roots, but highly expressed in other organs. Analysis of stress response processes revealed that all Lhc genes participate in at least one stress response. Five Lhc genes were confirmed to appear to have expression change using qPCR analysis under high temperature and salt stress. Particularly, under downy mildew, root-knot nematode stresses, and blight stress, up-regulated Lhc genes were the most abundant ones, indicating that the Lhc family acts as a significant role in the growth and development of cucumber. These results provide valuable insights for further understanding the characteristics of the CsLhc family and analyzing the function of the Lhc family in cucumber resistance to biotic/abiotic stresses and in molecular breeding. Full article

Glycans on the surface of all immune cells are the product of diverse post-translational modifications (glycosylation) that affect almost all proteins and possess enormous structural heterogeneity. Their bioinformational content is decoded by glycan-binding proteins (lectins, GBPs), such as C-type lectins, including selectins, galectins, and Siglecs. Glycans located on the surface of immune cells are involved in many immunological processes through interactions with GBPs. Lectins recognize changes in the glycan epitopes; distinguish among host (self), microbial (non-self), and tumor (modified self) antigens; and consequently regulate immune responses. Understanding GBP–glycan interactions accelerates the development of glycan-targeted therapeutics in severe diseases, including inflammatory and autoimmune diseases and cancer. This review will discuss N- and O-glycosylations and glycosyltransferases involved in the biosynthesis of carbohydrate epitopes and address how interactions between glycan epitopes and GBPs are crucial in immune responses. The pivotal role of the glycan antigen tetrasaccharide sialyl Lewis x in mediating immune and tumor cell trafficking into the extravascular site will be discussed. Next, the role of glycans in modulating bacterial, fungal, viral, and parasitic infections and cancer will be surveyed. Finally, the role of glycosylation in antibodies and carbohydrate vaccines will be analyzed. Full article

The Japanese archipelago as a continental island of the Eurasia continent and harboring high levels of plant species diversity provides an ideal geographical setting for investigating vicariant allopatric speciation due to the sea-level fluctuations associated with climatic oscillations during the Quaternary. In this study, three chloroplast DNA regions and 14 nuclear loci were sequenced for 31 individuals from three populations of Torreya nucifera var. nucifera and 52 individuals from three populations of T. nucifera var. radicans. Population genetic analyses (Network, STRUCTURE and phylogeny) revealed that the genetic boundaries of the two varieties are distinct, with high genetic differentiation (F_ST) of 0.9619 in chloroplast DNA and 0.6543 in nuclear loci. The relatively ancient divergence times between the two varieties were estimated to 3.03 Ma by DIYABC and 1.77 Ma by IMa2 when dated back to the late Pliocene and the early Pleistocene, respectively. The extremely weak gene flow (2Nm = 0.1) between the two varieties was detected by IMa2, which might be caused by their population expansion since the early Pleistocene (~2.0 Ma) inferred in the Bayesian skyline plots and DIYABC. Niche modeling showed that the two varieties had significant ecological differentiation (p < 0.001) since the Last Interglacial even earlier. These results demonstrate that vicariant allopatric speciation due to sea-level fluctuations may be a common mode of speciation in the Japanese archipelago. This finding provides insights into the understanding of species diversification in the Japanese Archipelago and even East Asian flora under climatic oscillations during the Quaternary. Full article

How cognitive limitations of individuals may affect the dynamics of cultural evolution under the effects of economic and technological forces is explored here. In particular, the extraordinary economic growth during the industrial and scientific revolutions of the last two centuries has been accompanied by an extraordinary acceleration of cultural changes. We will propose that these changes are due to competition, decay and replacement processes among the different kinds of cultural contents, ultimately resulting from our cognitive limitations. Different laws have been proposed recently for the decay of individualized cultural items and for the underlying competition processes, which will be discussed herein. With respect to the informational/cognitive limitations of individuals, the cognitive psychology views will be complemented—and somehow quantified—from the angle of the “social brain” or “sociotype” hypothesis. The generational phenomenon also emerges, by which differentiated generations develop a remarkable divergence in ways of life, aspirations, ideals, values, and often in the use of communication technologies. It is in this interactive individual–generational context of competitive processes that the acceleration of cultural change during the few last decades might be investigated by considering the vastly increased economic output and the widespread use of new communication technologies. Full article

The basic helix–loop–helix (bHLH) family members are involved in plant growth and development, physiological metabolism, and various stress response processes. Pinus massoniana is a major turpentine-producing and wood-producing tree in seasonally dry areas of southern China. Its economic and ecological values are well known. The forestry industry holds it in exceptionally high regard. Drought severely limits the growth and productivity of P. massoniana, and the functional role of PmbHLH58 in drought stress is not clear. Therefore, PmbHLH58 was cloned from P. massoniana and its bioinformation was analyzed. Subcellular mapping of the gene was performed. The biological function of PmbHLH58 overexpression in Populus davidiana × P. bolleana was studied. The results show that the drought tolerance of PmbHLH58-overexpressed poplar was significantly improved, which may be due to the increase in water use efficiency and reactive oxygen species (ROS) accumulation under drought stress. In an ethylene-responsive manner, PmERF71 interacted with the PmbHLH58 protein, which was found by yeast two-hybridization. We further demonstrated that the drought-induced PmbHLH58 transcription factor increased the expression of key enzyme genes in ABA receptor family genes in PmbHLH58-overexpressing poplar lines (OE). These findings provide new insights into transcriptional regulation mechanisms related to drought stress and will promote the progression of the genetic improvement and plantation development of P. massonsiana. Full article

When classifying breeds of dogs, the accuracy of classification significantly affects breed identification and dog research. Using images to classify dog breeds can improve classification efficiency; however, it is increasingly challenging due to the diversities and similarities among dog breeds. Traditional image classification methods primarily rely on extracting simple geometric features, while current convolutional neural networks (CNNs) are capable of learning high-level semantic features. However, the diversity of dog breeds continues to pose a challenge to classification accuracy. To address this, we developed a model that integrates multiple CNNs with a machine learning method, significantly improving the accuracy of dog images classification. We used the Stanford Dog Dataset, combined image features from four CNN models, filtered the features using principal component analysis (PCA) and gray wolf optimization algorithm (GWO), and then classified the features with support vector machine (SVM). The classification accuracy rate reached 95.24% for 120 breeds and 99.34% for 76 selected breeds, respectively, demonstrating a significant improvement over existing methods using the same Stanford Dog Dataset. It is expected that our proposed method will further serve as a fundamental framework for the accurate classification of a wider range of species. Full article

Rubus idaeus is one of the primary cultivated species of raspberries, renowned for its appealing color, distinctive flavor and numerous health benefits. WIP proteins, which contain three conserved amino acids (W: Tryptophan, I: Isoleucine, P: Proline) and four zinc finger motifs in a highly conserved C-terminal region, are members of the A1d subgroup of C2H2 zinc finger proteins. Drought is one of the main limiting factors of plant growth and development, which restricts the cultivation and utilization of raspberry in northwest China. In this study, to obtain candidate genes for drought resistance, we identified key related genes, RiWIPs, from R. idaeus and analyzed their bioinformation and tissue stress response expression to drought. We found that there are three RiWIPs in R. idaeus and they are located on chromosomes 3, 4 and 6 of R. idaeus, respectively. The open reading frames (ORFs) of the RiWIPs ranged from 870 to 1056 bp in length, encoding 289 to 372 amino acid residues. The proteins were highly conserved and feature diverse conserved motifs. The promoters of the RiWIPs contained abundant cis-elements related to growth, development and stress response. Tissue-specific expression analysis revealed that the RiWIPs were expressed in the leaves, stems and roots of both drought-susceptible and drought-tolerant cultivars, except for RiWIP2, which was only expressed in the roots of the drought-tolerant one. Under drought stress, the transcriptional activity of the RiWIPs was increased to different degrees with specificity in the leaves, stems and roots. Our study demonstrated the role of WIP genes in raspberry drought response and provided a marker gene, RiWIP2, for drought resistance and candidate genes for subsequent drought-resistant breeding of R. idaeus. Full article

Objectives. Brain–behavior connections are a new means to evaluate sports performance. This electroencephalogram (EEG) study aims to estimate endurance exercise performance by investigating eigenvalue trends and comparing their sensitivity and linearity. Methods. Twenty-three cross-country skiers completed endurance cycling tasks. Twenty-four-channel full-brain EEG signals were recorded in the motor phase and recovery phase continuously. Eighteen EEG eigenvalues calculation methods were collected, commonly used in previous research. Time-frequency, band power, and nonlinear analyses were used to calculate the EEG eigenvalues. Their regression coefficients and correlation coefficients were calculated and compared, with the linear regression method. Results. The time-frequency eigenvalues shift slightly throughout the test. The power eigenvalues changed significantly before and after motor and recovery, but the linearity was not satisfactory. The sensitivity and linearity of the nonlinear eigenvalues were stronger than the other eigenvalues. Of all eigenvalues, Shannon entropy showed completely non-overlapping distribution intervals in the regression coefficients of the two phases, which were −0.1474 ± 0.0806 s⁻¹ in the motor phase and 0.2560 ± 0.1365 s⁻¹ in the recovery phase. Shannon entropy amplitude decreased more in the F region of the brain than in the other regions. Additionally, the higher the level of sport, the slower the decline in Shannon entropy of the athlete. Conclusions. The Shannon entropy method provided more accurate estimations for endurance exercise performance compared to other eigenvalues. Full article

Agave is a significant fiber crop in tropical regions, known for its high fiber strength. Lignin is closely associated with fiber strength, and phenylalanine ammonia-lyase (PAL) serves as the initial enzyme in biosynthesis of lignin. Hence, it is of considerable significance to study the genes of PAL family to analyze the characteristics and mechanism of sisal fiber development. In this research, we conducted a transcriptomic analysis of Agave schidigera, a widely recognized ornamental plant in agave. Approximately 29.85 million clean reads were acquired through Illumina sequencing. In total, 116,602 transcripts including 72,160 unigenes were assembled, and 22.06~63.56% of those unigenes were annotated in public databases. Two, six, six and six PAL genes were successfully identified and cloned from A. schidigera, A. deserti, A. tequilana and A. H11648, respectively. After phylogenetic analysis, these genes were clustered into two branches. Genes AhPLA2a and AhPLA2c exhibited higher expression levels compared to other genes but had different expression patterns. Moreover, AhPLA2a and AhPLA2c were expressed at high levels under full-nutrient, nitrogen-free and phosphorus-free stresses. Most PAL genes were induced by Phytophthora nicotianae Breda, especially AhPAL1a, AhPAL1b, AhPAL2b and AhPAL2c. This research is the first work to present a de novo transcriptome dataset for A. schidigera, enriching its bioinformation of transcripts. The cloned PAL genes and the expression analyses will form the basis of future research on lignin biosynthesis, the relationship between lignin and fiber strength, and stress resistance in Agave species. Full article

The Remorin (REM) gene family is a plant-specific, oligomeric, filamentous family protein located on the cell membrane, which is important for plant growth and stress responses. In this study, a total of 22 PtREMs were identified in the genome of Populus trichocarpa. Subcellular localization analysis showed that they were predictively distributed in the cell membrane and nucleus. Only five PtREMs members contain both Remorin_C- and Remorin_N-conserved domains, and most of them only contain the Remorin_C domain. A total of 20 gene duplication pairs were found, all of which belonged to fragment duplication. Molecular evolutionary analysis showed the PtREMs have undergone purified selection. Lots of cis-acting elements assigned into categories of plant growth and development, stress response, hormone response and light response were detected in the promoters of PtREMs. PtREMs showed distinct gene expression patterns in response to diverse stress conditions where the mRNA levels of PtREM4.1, PtREM4.2 and PtREM6.11 were induced in most cases. A co-expression network centered by PtREMs was constructed to uncover the possible functions of PtREMs in protein modification, microtube-based movement and hormone signaling. The obtained results shed new light on understanding the roles of PtREMs in coping with environmental stresses in poplar species. Full article

Aviation information systems are a key component in ensuring efficient and smooth air transport operations. In this regard, the transfer of passenger information between parties is of paramount importance. With the continuous improvement of biometrics technology, this kind of individual identification that can provide accurate and unforgeable identification is widely used in various fields. This research presents the significance and effective application scenarios of facial recognition in biometrics in air transport operations. Due to the characteristics of aviation information systems, Distributed Ledger Technology (DLT) is used in this study for secure and private transmission of facial recognition information. Distributed systems can give a transparent and secure platform to multiple parties to access sensitive passenger data. This study uses the Corda framework as the DLT that supports CorDapp development. Based on the above techniques, this study proposes two feasible application scenarios. One is a baggage match detection system to prevent misplaced baggage, and the other is an iAPIS system that transmits passenger information in real-time communication between airlines and border control agencies. This article details how to apply the research in these two scenarios, as well as the benefits and implications of the applications. Finally, this article presents an outlook for future development and feasible directions for improvement. Full article

The areas of the Mount Aso grasslands in Kumamoto, Japan, are the primary location for the breeding of the Kumamoto strain of Japanese Brown cattle (JBRK). Although Aso limonite, deposited by volcanic ash and magma, has been commonly fed to pregnant JBRK in this area, the mechanisms of its salutary effects on pregnant JBRK have not yet been elucidated. Approximately 100 days before the expected day of calf delivery, seven JBRK (four supplemented with limonite and three controls without limonite) were assigned to this study, from which a buccal swab was collected at the highest rumination every 30 days for 90 days. DNA extracted from these swabs was then analyzed using a 16S rRNA gene amplicon sequence analysis. Statistically significant differences between the two groups were discovered through beta-diversity analysis, though results from alpha-diversity analysis were inconclusive. The microbiota identified were classified into six clusters, and three of the main clusters were core-rumen bacteria, primarily cellulose digestion in cluster 1, oral bacteria in cluster 2, and non-core-rumen bacteria in cluster 3. In the limonite group, core-rumen bacteria decreased while non-core-rumen bacteria increased, suggesting that limonite feeding alters rumen microbiota, particularly activation of non-core-rumen microbiota. Full article