Search Results (74)

Background/Objectives: DNA-damaging agents can contribute to genetic instability, and such agents are often used in cancer chemotherapeutic regimens due to their cytotoxicity. Thus, understanding the mechanisms involved in DNA damage processing can not only enhance our knowledge of basic DNA repair mechanisms but may also be used to develop improved chemotherapeutic strategies to treat cancer. The high-mobility group box protein 1 (HMGB1) is a known nucleotide excision repair (NER) cofactor, and its family member HMGB3 has been implicated in chemoresistance in ovarian cancer. Here, we aim to understand the potential role(s) of HMGB3 in processing DNA damage. Methods: A potential role in NER was investigated using HMGB3 knockout human cell lines in response to UV damage. Subsequently, potential roles in DNA interstrand crosslink (ICL) and DNA double-strand break (DSB) repair were investigated using mutagenesis assays, metaphase spreads, foci formation, a variety of DNA repair assays, and TagSeq analyses in human cells. Results: Interestingly, unlike HMGB1, HMGB3 does not appear to play a role in NER. We found evidence to suggest that HMGB3 is involved in the processing of both DSBs and ICLs in human cells. Conclusions: These novel results elucidate a role for HMGB3 in DNA damage repair and, surprisingly, also indicate a distinct role of HMGB3 in DNA damage repair from that of HMGB1. These findings advance our understanding of the role of HMGB3 in chemotherapeutic drug resistance and as a target for new chemotherapeutic strategies in the treatment of cancer. Full article

Botryosphaeria dothidea is the causative agent of Chinese hickory trunk canker, which poses significant threat to the production of Chinese hickory (Carya cathayensis Sarg.). Previous studies reported that endophytic–pathogenic phase transition, also referred to as latent infection, plays an important role in the interaction of Botryosphaeria dothidea with various host plants, including Chinese hickory. However, the mechanism underlying this phase transition is not well understood. Here, we employed RNA-Seq to investigate transcriptional changes in B. dothidea during its phase transition upon interaction with Chinese hickory. A co-expression network was generated based on 6391 differentially expressed genes (DEGs) identified from different infection stages and temperature treatments. One co-expressed module was found that highly correlated with temperature treatments which simulated conditions of B. dothidea latent infection in the field. Subsequently, 53 hub genes were detected, and gene ontology (GO) enrichment analysis revealed three categories of enriched GO terms: transmembrane transport or activity, ion homeostasis or transport, and carbohydrate metabolism. One PacC transcriptional factor (BDLA_00001555, an ambient pH regulator), and one endo-β-1,3-glucanase (BDLA_00010249) were specifically upregulated under temperature treatments that corresponded with the activation stage of B. dothidea’s pathogenic state. The knockout mutant strain of BDLA_00001555 demonstrated defective capability upon the activation of the pathogenic state. This confirmed that BDLA_00001555, the PacC transcriptional factor, plays an important role in the latent infection phase of B. dothidea. Our findings provide insights into the pathogenic mechanism of Chinese hickory trunk canker disease. Full article

Grafting involves complex hormonal interactions at graft interfaces that are not yet fully understood. In this study, we analyzed hormone fluctuations and gene expression during callus proliferation and vascular tissue differentiation in hickory (Carya cathayensis Sarg.) grafts. Cytokinin and ethylene precursor ACC levels steadily increased after grafting. The biosynthetic genes for these hormones (IPT3, ACS1, ACO1, and ACO5) exhibited heightened expression. Genes related to cytokinin signaling (RR3, ARR4, and ZFP5) and ethylene signaling (MKK9, ESE1, and ESE3) were similarly upregulated. Conversely, genes associated with jasmonic acid, abscisic acid, and strigolactone pathways were downregulated, including synthesis genes (AOC4 and AOS) and those involved in signal transduction (NAC3, WRKY51, and SMAX1). Correspondingly, JA-Ile and 5-deoxystrigol levels significantly decreased. Indole-3-acetic acid (IAA) levels also dropped during the early stages of graft union formation. These results suggest that low auxin concentrations may be essential in the initial stages after grafting to encourage callus proliferation, followed by an increase at later stages to facilitate vascular bundle differentiation. These findings imply that maintaining a balance between low auxin levels and elevated cytokinin and ethylene levels may be critical to support cell division and callus formation during the initial proliferation phase. Later, during the vascular differentiation phase, a gradual rise in auxin levels, accompanied by elevated ethylene, may facilitate the differentiation of vascular bundles in hickory grafts. Full article

Accurate tree species identification through bark characteristics is essential for effective forest management, but traditionally requires extensive expertise. This study leverages artificial intelligence (AI), specifically the EfficientNet-B3 convolutional neural network, to enhance AI-based tree bark identification, focusing on northern red oak (Quercus rubra), hackberry (Celtis occidentalis), and bitternut hickory (Carya cordiformis) using the CentralBark dataset. We investigated three environmental variables—time of day (lighting conditions), bark moisture content (wet or dry), and cardinal direction of observation—to identify sources of classification inaccuracies. Results revealed that bark moisture significantly reduced accuracy by 8.19% in wet conditions (89.32% dry vs. 81.13% wet). In comparison, the time of day had a significant impact on hackberry (95.56% evening) and northern red oak (80.80% afternoon), with notable chi-squared associations (p < 0.05). Cardinal direction had minimal effect (4.72% variation). Bitternut hickory detection consistently underperformed (26.76%), highlighting morphological challenges. These findings underscore the need for targeted dataset augmentation with wet and afternoon images, alongside preprocessing techniques like illumination normalization, to improve model robustness. Enhanced AI tools will streamline forest inventories, support biodiversity monitoring, and bolster conservation in dynamic forest ecosystems. Full article

Garvin Heights Park in southeastern Minnesota, USA, is a 12 ha mosaic of bluff prairie, oak savanna, and oak–hickory woodland co-owned by the City of Winona and Winona State University, with a 40+ year history of encroachment by non-native woody invasives, especially buckthorn (Rhamnus cathartica) and honeysuckles (Lonicera spp.). Habitat restoration was initiated in the early 1990s, but management gaps and a seedbank of invasives compromised initial efforts. More consistent and sustainable restoration activities since 2016 have included cutting and chemical treatment of invasives, managed goat browsing, targeted reseeding and plug planting with native species, and more regular prescribed fires. Throughout the restoration process, we assessed changes in buckthorn densities in response to various management practices, assessed the restored savanna tree community, and documented the presence of blooming plants across all park habitats. Manual clearing of woody invasives and repeated goat browsing significantly reduced buckthorn and honeysuckle abundance in prairies and savannas. Park plant communities responded to the combination of management strategies with reduced densities of woody invasives and expanding diversity (currently >220 species present) of forbs and grasses, including a large and growing population of state-threatened Great Indian Plantain (Arnoglossum reniforme). Prescribed fires have benefitted prairies but have done little to improve savanna plant communities, due largely to excessive tree canopy coverage causing a lack of burnable fuels (i.e., dry forbs and grasses). Improved partnerships between landowners and dedicated volunteers are working to expand restoration efforts to include other portions of the park and adjacent woodlands. Full article

The structural characteristics of hickory trees exhibit a significant correlation with their fruit yield. As a distinctive high-quality nut of Zhejiang Province, hickory is a unique high-end dry fruit and woody oil plant in China. However, the long growth cycle and extended maturation period make their management particularly challenging, especially in the absence of high-precision 3D digital models. This study aims to optimize hickory tree management and identify trees with the most optimal structural features. It employs gradient-boosted machine learning modeling based on 23 key tree characteristics, transforming the experiential knowledge of forest farmers into quantifiable parameters. The consensus model achieved an LOOCV average accuracy of 87%, a training set accuracy of 100%, and a test set accuracy of 78%. Through this approach, three structural parameters that significantly impact the hickory tree were identified: the number of branches, the total length of all branches, and the crown base height from the ground. These parameters were used to select trees with superior structural traits. Furthermore, a novel method based on distance metrics was developed to assess the structural similarity of trees. This research not only highlights the importance of incorporating tree structural characteristics into forest management practices but also demonstrates how modern technological tools can enhance the productivity and economic returns of hickory forests. Through this integration, both the sustainability and economic viability of hickory forests are improved. Full article

On 14 December 2005, there was a catastrophic flood after a failure in the upper reservoir at the Taum Sauk Plant in southern Missouri. While there has been extensive research on the cause of the dam’s failure and the flood’s immediate impact, there has been limited investigation on how vegetation in and around the resulting flood scour has changed since this event. This study fills this gap through a time-series analysis using imagery sourced from GloVis and Planet Explorer to quantify vegetation levels prior to the flood (2005) through to 2024. Vegetation level was calculated using the Normalized Difference Vegetation Index (NDVI), which measures the level of greenness via light reflected by vegetation. Vegetation levels inside of the scour were compared to two 120 m buffer areas surrounding the scour, immediately adjacent (0–120 m) and at 120–240 m from the scour’s edge. Within the scour, NDVI analysis showed a dramatic loss of vegetation immediately after the flood, followed by varying levels for several years, before a steady increase in the proportion of areas with vegetation starting in 2014. The buffer area adjacent to the edge of the scour showed a similar pattern, but at lower magnitudes of change, which likely reflects the ragged edge created by the flood. The buffer area farther from the edge showed a consistent pattern of high vegetation, which likely reflects the broader landscape. While ground truthing confirmed these patterns between 2006 and 2011, in 2012, the ground truthing revealed much recovery in small local areas within the scour that were not apparent though NDVI analysis. These local areas of recovery were reflected in the pattern of recolonization of the scour from nearby glades (i.e., natural habitats of exposed bedrock) by glade flora and by the eastern collared lizard (Crotaphytus collaris collaris), an apex predator adapted to living in rocky, open areas and a bioindicator of vegetation recovery. While recovery of vegetation occurred steadily after 2012, ground truthing indicated that the original oak/hickory forest was now a minor component of this recovery, and that glade species dominated the former forested area. Full article

Finding appropriate shaking parameters is crucial in designing effective mechanical harvesters. The maximum fruit removal can be achieved when the machine operator properly adjusts the amplitude and frequency for shaking each tree. This review covers the progress in research and development over the past decades on using mechanical harvesters for nut trees, such as almonds, pistachios, walnuts, and hickories, with a specific focus on the natural frequency of individual trees. Furthermore, the reported values of shaking frequency and amplitude from previous studies were discussed and compared, along with frequency calculation approaches based on various shaking mechanisms. Additionally, other parameters, such as clamping force, height, and shaking amplitude, were investigated to determine optimal values for minimizing tree damage. This review emphasizes that the tree’s diameter, height, and canopy morphology should be the primary factors considered when estimating the optimal shaking frequency for nut trees. It also highlights that, to date, the shaking amplitude, frequency, and duration set by field managers or machine operators tend to remain consistent for all trees, which can limit harvesting efficiency. The findings suggest that selecting these parameters uniformly across all trees may not result in efficient fruit removal for individual trees. However, with the assistance of modern computing technology and its adaptation for in-field applications, it is feasible to determine the optimal shaking frequency for each tree mathematically. This approach can maximize fruit removal rates while minimizing tree damage. Finally, the review suggests that improving existing harvesting machines by incorporating better vibratory patterns could offer benefits such as enhanced productivity, reduced labor costs, and decreased permanent tree damage. Full article

Chinese hickory (Carya cathayensis) is an important tree species for agriculture, but dry rot disease, caused by Botryosphaeria dothidea, threatens its viability. To study the interactions between the tree and the pathogen, transcriptomic sequencing was conducted on infected and healthy tissues from field-grown hickory. Differential gene expression analysis identified key defense pathways and genes activated during infection. The study also explored the roles of non-coding RNAs, such as lncRNAs and circRNAs, in the tree’s defense. The results showed that during the early and mid stages of infection, the tree defends itself through mechanisms like enhanced lignin synthesis and increased peroxidase activity. Non-coding RNAs contribute to disease resistance by reinforcing the cell wall, increasing oxidase activity, and promoting the synthesis of antibiotic-related secondary metabolites. Additionally, gene expression patterns at these stages differ significantly from those at the late stage of infection, when most disease resistance pathways are suppressed, and genes like PR1 and WRKY2 show a decline. These findings offer valuable insights into the pathogenesis of Chinese hickory dry rot disease and potential strategies for improving resistance. Full article

Carya dabieshanensis is a species of significant economic value due to its unique flavor and nutritional properties as a snack food, as well as its durable wood, which is highly suitable for furniture production. Known for its remarkable adaptability to environmental stress, this species serves as a valuable genetic resource for enhancing hickory cultivars. However, its restricted distribution and limited availability of high-quality germplasm have impeded large-scale cultivation and hindered industry development. While the genetic diversity and genomic basis of its environmental adaptation hold great promise for future breeding programs, no studies to date have utilized SNP markers to explore its genetic diversity or the genomic mechanisms underlying environmental adaptability. In this study, we analyzed 60 samples from 12 natural populations of C. dabieshanensis, representing its global distribution. Using the Carya illinoinensis (Wangenh. and K. Koch) genome as a reference, we employed Specific Locus Amplified Fragment Sequencing (SLAF-seq) to generate high-quality SNP data. By integrating population and landscape genomics approaches, we investigated the genetic structure and diversity of wild populations and identified key environmental factors driving genetic differentiation. Our population genomics analysis revealed 9,120,926 SNP markers, indicating substantial genetic diversity (π = 1.335 × 10⁻³ to 1.750 × 10⁻³) and significant genetic differentiation among populations (F_ST = 0.117–0.354). Landscape genomics analysis identified BIO3 (Isothermality), BIO6 (Min Temperature of Coldest Month), and BIO14 (Precipitation of Driest Month) as critical environmental factors shaping genetic diversity. This study provides essential insights into the genetic resources of C. dabieshanensis, facilitating the development of climate-resilient cultivars and offering a scientific foundation for the conservation and sustainable management of its wild populations. Full article

Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination antiretroviral therapy (cART), though certain oral manifestations persist despite therapy. Microorganisms associated with oral cavity opportunistic infections in patients with HIV cause similar pathologies in cats. To further develop this model, we evaluated characteristics of feline oral health and the oral microbiome during experimental FIV infection over an 8-month period following cART. Using 16S rRNA sequencing, we evaluated gingival bacterial communities at four timepoints in uninfected and FIV-infected cats treated with either cART or placebo. Comprehensive oral examinations were also conducted by a veterinary dental specialist over the experimental period. Gingival inflammation was higher in FIV-infected cats treated with placebo compared to cART-treated cats and the controls at the study endpoint. Oral microbiome alpha diversity increased in all groups, while beta diversity differed among treatment groups, documenting a significant effect of cART therapy on microbiome community composition. This finding has not previously been reported, and indicates cART ameliorates immunodeficiency virus-associated oral disease via the preservation of oral mucosal microbiota. Further, this study illustrates the value of the FIV animal model for investigations of mechanistic associations and therapeutic interventions for HIV’s oral manifestations. Full article

Phytophthora cinnamomi causes significant root rot in hickory, leading to substantial yield losses. While Bacillus spp. are recognized as beneficial rhizosphere microorganisms, their application against hickory root rot and their impact on rhizosphere microbial communities remain under-investigated. This study demonstrated that Bacillus velezensis TCS001 significantly inhibited P. cinnamomi ST402 growth in vitro, and achieved 71% efficacy in root rot disease management. Scanning electron microscopy (SEM) revealed that TCS001 fermentation filtrate induced mycelial deformities in P. cinnamomi. An analysis of α and β diversity indicated a significant impact of TCS001 on rhizosphere bacterial community richness and diversity, with minimal effects on the fungal community. Moreover, TCS001 altered the hickory rhizosphere microbiome co-occurrence network. The differential abundance analysis suggests that TCS001 promotes the recruitment of beneficial microbes associated with disease resistance, thereby suppressing disease development. These findings underscore the influence of TCS001 on the hickory rhizosphere microbiome in the presence of pathogens, providing valuable data for future research and the development of effective biocontrol strategies for hickory root rot. Full article

Managing forest understory has a significant impact on soil greenhouse gas (GHG) emissions and the ecosystem’s capacity for carbon sequestration. However, its specific impacts and mechanisms within hickory (Carya cathayensis Sarg) forests remain unclear. The objective of this study was to examine the effects of different understory vegetation treatments on hickory stands with similar growth history, site conditions, and slopes: Cinnamomum chekiangense (Cinnamomum chekiangense Nakai) and strip-sown ryegrass (Lolium perenne L.) (CR1), Cinnamomum chekiangense and scattered ryegrass (CR2), Torreya grandis (Torreya grandis’ ‘Merrillii’ Hu) and strip-sown wild rapeseed (Brassica napus L.) (TW1), Torreya grandis and scattered wild rapeseed (TW2), and removal of understory vegetation (CK). Twenty experimental plots were established at the Lin’an Forestry Carbon Sink Pioneer Base, and after 12 months of monitoring, the responses of GHG emissions, vegetation, and soil organic carbon (SOC) sequestration were analyzed, revealing the differences in ecosystem carbon sequestration capacity. Compared to CK, CR1, CR2, TW1, and TW2 increased the global warming potential (GWP) by approximately 26%, 55%, 26%, and 16%, respectively. The SOC increased by approximately 76%, 102%, 51%, and 32%, respectively, while the vegetation carbon sink increased by approximately 30%, 27%, 53%, and 62%, respectively. In summary, ecosystem carbon sequestration increased by approximately 109%, 98%, 95%, and 92%, respectively. The findings indicate that managing understory vegetation in pecan forests significantly enhances ecosystem carbon sequestration but also increases soil GHG emissions. To enhance future research priorities, it is essential to focus on increasing carbon sequestration in hickory forests and managing soil GHG emissions through effective and rational understory vegetation management. Full article

Amidst the global shift towards a low-carbon development trajectory, the hickory industry in Lin’an District is progressively embracing green, low-carbon, and sustainable practices. This study, leveraging the life cycle assessment (LCA) methodology, meticulously scrutinizes the carbon footprint of the hickory industry by segmenting its life cycle into two distinct subsystems: the plantation and the factory. Through comprehensive, year-long monitoring of soil greenhouse gas (GHG) emissions in hickory plantations, our findings underscore that while total GHG emissions from eco-complex management (ECM) surpassed those of intensive management (IM) by 10.7% (p < 0.001), ECM significantly mitigated the carbon footprint per kilogram of hickory produced, achieving a reduction of 1.0495 kgCO₂eq. This advantage is primarily attributable to ECM’s diminished reliance on chemical fertilizers. Within the factory subsystem, when processing 1 kg of hickory, the digital factory incurred a carbon footprint of 2.5923 kgCO₂eq kg⁻¹, whereas family workshops exhibited a lower footprint of 1.9544 kgCO₂eq kg⁻¹. Notably, the processing and packaging stages collectively accounted for over 90% of the factory subsystem’s carbon emissions, with natural gas being the primary contributor during processing. To estimate the carbon emission reduction potential within the hickory industry, this research draws parallels with emission reduction strategies employed by other industries and outlines tailored strategies to propel its low-carbon development. By advocating for the widespread adoption of ECM and enhancing the energy efficiency of processing enterprises, the hickory industry can effectively diminish its carbon footprint and steer towards a green, low-carbon, and high-quality development paradigm. Full article

Accurate scientific information is critical for undertaking appropriate conservation and management practices for imperiled species. One source of concern is that research findings might vary for non-biological reasons, including experimental design and analytical methods. To illustrate, we provide detailed modern analysis of reproductive data for leatherback turtles (Dermochelys coriacea). This species exhibits significant fluctuations in nesting densities across different regions, possibly driven by local rather than global factors. Key factors influencing these changes include hatching success and sex determination, both sensitive to incubation temperatures (e.g., lower temperatures yield more males, higher temperatures yield females). This study updates the understanding of temperature-dependent sex determination (TSD) in this species using Bayesian statistics. Growth rate data from the West Pacific and Northwest Atlantic populations show a similar, monotone increase with temperature, affirming the reliability of the models used. The analysis of TSD patterns indicates that observed differences are more likely due to study methodologies and clutch-specific factors rather than regional differences. These findings challenge previous assumptions, showing that leatherback TSD does not conform to a simple on/off pattern but is influenced by multiple, interacting environmental factors. Population dynamics models must account for these complexities, recognizing that both sex ratios and hatching success are critical to understand the rapid changes observed in some leatherback populations. Full article