Search Results (65)

Background: Centromeric alpha satellite DNA is organized into higher-order repeats (HORs), whose precise structure is often difficult to resolve in standard genome assemblies. The recent telomere-to-telomere (T2T) assembly of the human genome enables complete analysis of centromeric regions, including the full structure of HOR arrays. Methods: We applied the novel high-precision GRMhor algorithm to the complete T2T-CHM13 assembly of human chromosome 21. GRMhor integrates global repeat map (GRM) and monomer distance (MD) diagrams to accurately identify, classify, and visualize HORs and their subfragments. Results: The analysis revealed a novel Cascading 11mer HOR array, in which each canonical HOR copy comprises 11 monomers belonging to 10 different monomer types. Subfragments with periodicities of 4, 7, 9, and 20 were identified within the array. A second, complex 23/25mer HOR array of mixed Willard’s/Cascading type was also detected. In contrast to the hg38 assembly, where a dominant 8mer and 33mer HOR were previously annotated, these structures were absent in the T2T-CHM13 assembly, highlighting the limitations of hg38. Notably, we discovered a novel 52mer HOR—the longest alpha satellite HOR unit reported in the human genome to date. Several subfragment repeats correspond to alphoid subfamilies previously identified using restriction enzyme digestion, but are here resolved with higher structural precision. Conclusions: Our findings demonstrate the power of GRMhor in resolving complex and previously undetected alpha satellite architectures, including the longest canonical HOR unit identified in the human genome. The precise delineation of superHORs, Cascading structures, and HOR subfragments provides unprecedented insight into the fine-scale organization of the centromeric region of chromosome 21. These results highlight both the inadequacy of earlier assemblies, such as hg38, and the critical importance of complete telomere-to-telomere assemblies for accurately characterizing centromeric DNA. Full article

Repetitive DNA represents over 50% of the human genome and is an abundant component of circulating cell-free DNA (cfDNA). We previously showed that cfDNA levels and integrity can predict survival in elderly patients with cardiovascular disease. Here, we aimed to clarify whether a low-pass next-generation sequencing (NGS) approach can characterize the repeat content of cfDNA. Considering the bimodal distribution of cfDNA fragment lengths, we examined the occurrence of repetitive DNA subfamilies separately in dinucleosomal (>250 bp) and mononucleosomal (≤250 bp) cfDNA sequences from 24 patients admitted for heart failure. An increase in the relative abundance of Alu repetitive elements was observed in the longer fraction, while alpha satellites were enriched in the mononucleosomal fraction. The relative abundance of Alu, ALR, and L1HS DNA in the dinucleosomal fraction correlated with different prognostic biomarkers, and Alu DNA was negatively associated with the presence of chronic kidney disease comorbidity. These results, together with the observed inverse correlation between Alu DNA abundance and cfDNA integrity, suggest that the composition of plasma cfDNA could be determined by multiple mechanisms in different physio-pathological conditions. In conclusion, low-pass NGS is an inexpensive method to analyze the cfDNA repeat landscape and identify new cardiovascular disease biomarkers. Full article

MSTN has been used as a candidate gene in the genetics, breeding, and improvement of animal breeds. However, the possible mechanism by which the MSTN gene regulates muscle development through PSMA6 is not well understood. Previous methylome and transcriptome sequencing analyses of gluteal muscle tissues from MSTN+/−Luxi cattle and wild-type Luxi cattle identified that the PSMA6 gene exhibited a negative correlation between methylation levels and transcriptional activity. To investigate whether MSTN expression regulates PSMA6 gene expression, we examined the effects of MSTN on DNA methyltransferases (DNMT1, DNMT2, DNMT3A, and DNMT3B) and DNA demethylases (TET1, TET2, and TET3). Additionally, chromatin immunoprecipitation (ChIP) assays were performed to detect the binding interaction between PSMA6 and TET2. In this paper, we first established an MSTN knockdown cellular model to preliminarily validate its regulatory effect on PSMA6 expression. Subsequently, the developmental impact of PSMA6 on bovine skeletal muscle satellite cells was further investigated through both knockdown and overexpression of the PSMA6 gene. Furthermore, we examined changes in the expression of key components of the AKT/mTOR signaling pathway to elucidate the mechanisms underlying the PSMA6-mediated regulation of satellite cell development. The results demonstrate that myostatin (MSTN) inhibition significantly decreased proteasome 20S subunit alpha-6 (PSMA6) gene expression, while increasing demethylase expression, particularly ten-eleven translocation-2 (TET2), which exhibited the most pronounced changes. During the cell proliferation stage, the markers Paired Box 7 (PAX7) and Ki-67 exhibited no significant changes, whereas the PSMA6 gene was either overexpressed or disrupted. Conversely, PSMA6 overexpression altered the myogenic differentiation markers, causing the differential regulation of myosin heavy chain (MyHC) and myogenin (MyoG) expression, with MyHC upregulation and concurrent MyoG downregulation. PSMA6 gene overexpression led to the downregulation of AKT1 and Rac1, as well as the activation of the AKT/mTOR pathway, including key factors such as mTOR, p-mTOR, RPS6, p-RPS6, and RhoA. PSMA6 interference resulted in the downregulation of p-mTOR and the upregulation of p-RPS6. Gene expression profiling in our study revealed that the myostatin (MSTN) knockout model significantly reduced the transcriptional levels of the proteasome α6 subunit (PSMA6) (p < 0.05), with the regulatory intensity showing a significant negative correlation with MSTN expression. This molecular evidence substantiates a negative regulatory axis between MSTN and PSMA6. Functional experiments demonstrated that PSMA6 overexpression specifically enhanced myotube formation rates in bovine skeletal muscle satellite cells, whereas siRNA-mediated PSMA6 knockdown exhibited no significant effects on cellular proliferation, indicating the functional specificity of this gene in myogenic differentiation. Mechanistic investigations further revealed that PSMA6 activates the canonical AKT/mTOR signaling transduction cascade through the phosphorylation of AKT and its downstream effector mTOR, thereby mediating the expression of myogenic regulatory factors MyoD and myogenin. Collectively, these findings demonstrate that MSTN deficiency alleviates the transcriptional repression of PSMA6, remodels skeletal muscle differentiation-associated signaling networks, and ultimately drives the directional differentiation of satellite cells toward myofiber specification. Full article

Lettuce (Lactuca sativa L.) plants showing leaf curl and vein enation symptoms were found in Yunnan province, China. PCR detection with genus-specific primers revealed that symptomatic lettuce plants were infected with Begomovirus. The full-length viral component and satellite molecules were obtained by RCA, restriction enzyme digestion, PCR, cloning and DNA sequencing. A viral component (YN-2023-WJ) and three satellite molecules (YN-2023-WJ-alpha1, YN-2023-WJ-alpha2 and YN-2023-WJ-beta) were obtained from diseased lettuce plants. YN-2023-WJ exhibited the highest nt identity at 97.1% with pepper leaf curl Yunnan virus isolated from cigar plants. YN-2023-WJ-beta displayed the highest nt identity at 93.9% with tomato leaf curl China betasatellite. YN-2023-WJ-alpha1 showed the highest nt identity at 94.7% with ageratum yellow vein alphasatellite. YN-2023-WJ-alpha2 shared the highest nt identity at 75.6% with gossypium mustelinum symptomless alphasatellite and vernonia yellow vein Fujian alphasatellite. Based on the threshold for the classification of Begomovirus, Betasatellite and Alphasatellite, YN-2023-WJ was designated as a new isolate of PepLCYnV, YN-2023-WJ-beta as a new isolate of ToLCCNB and YN-2023-WJ-alpha1 as a new member of AYVA, whereas YN-2023-WJ-alpha2 was identified as a new geminialphasatellite species, for which the name pepper leaf curl Yunnan alphasatellite (PepLCYnA) is proposed. To the best of our knowledge, this is the first report of L. sativa L. infection by PepLCYnV associated with ToLCCNB, AYVA and PepLCYnA, and L. sativa L. is a new host plant of Begomovirus. Full article

Depending on the method of cellulose production, the proportion of alpha fraction in it can vary significantly. Paper pulp, unlike dissolving cellulose, has an alpha proportion of less than 90%. The presence of cellulose satellites in the system does not impede the formation of concentrated solutions of N-methylmorpholine-N-oxide (NMMO). In the current study, spinning solutions based on cellulose with a low alpha fraction (up to 90%) (pulp cellulose) are investigated. The morphological features and rheological behavior of such solutions are examined. It is suggested to roll the obtained solutions in order to obtain cellulose membranes. X-ray diffraction, IR spectroscopy, AFM and SEM were used to investigate the resulting structure and morphology of the obtained membranes. It is shown that the degree of crystallinity for the membranes varies based on the impurity content in the sample. The morphology of the films is characterized by a dense texture and the absence of vacuoles. The highest strength and elastic modulus were found for membranes made of bleached hardwood sulfate cellulose, 5.7 MPa and 6.4 GPa, respectively. The maximum values of the contact angle (48°) were found for films with a higher proportion of lignin. The presence of lignin in the membranes leads to an increase in rejection for the anionic dyes Orange II and Remazol Brilliant Blue R. Full article

Developing the capacity to monitor species diversity worldwide is of great importance in halting biodiversity loss. To this end, remote sensing plays a unique role. In this study, we evaluate the potential of Global Ecosystem Dynamics Investigation (GEDI) data, combined with conventional satellite optical imagery and climate reanalysis data, to predict in situ alpha diversity (Species richness, Simpson index, and Shannon index) among tree species. Data from Sentinel-2 optical imagery, ERA-5 climate data, SRTM-DEM imagery, and simulated GEDI data were selected for the characterization of diversity in four study areas. The integration of ancillary data can improve biodiversity metrics predictions. Random Forest (RF) regression models were suitable for estimating tree species diversity indices from remote sensing variables. From these models, we generated diversity index maps for the entire Cerrado using all GEDI data available in orbit. For all models, the structural metric Foliage Height Diversity (FHD) was selected; the Renormalized Difference Vegetation Index (RDVI) was also selected in all species diversity models. For the Shannon model, two GEDI variables were selected. Overall, the models indicated performances for species diversity ranging from (R² = 0.24 to 0.56). In terms of RMSE%, the Shannon model had the lowest value among the diversity indices (31.98%). Our results suggested that the developed models are valuable tools for assessing species diversity in tropical savanna ecosystems, although each model can be chosen based on the objectives of a given study, the target amount of performance/error, and the availability of data. Full article

Cultured meat (CM) is derived from the in vitro myogenesis of muscle satellite (stem) cells (MSCs) and offers a promising alternative protein source. However, the development of a cost-effective media formulation that promotes cell growth has yet to be achieved. In this study, laxogenin (LAX) and 5-alpha-hydroxy-laxogenin (5HLAX) were computationally screened against myostatin (MSTN), a negative regulator of muscle mass, because of their antioxidant properties and dual roles as MSTN inhibitors and enhancers of myogenesis regulatory factors. In silico analysis showed LXG and 5HLXG bound to MSTN with binding free energies of −7.90 and −8.50 kcal/mol, respectively. At a concentration of 10 nM, LAX and 5HLAX effectively inhibited the mRNA and protein expressions of MSTN, promoted myogenesis, and enhanced myotube formation and maturation. In addition, by acting as agonists of ROS downregulating factors, they exhibited antioxidative effects. This study shows that supplementation with LAX or 5HLAX at 10 nM in CM production improves texture, quality, and nutritional value. We believe this study fills a research gap on media development for myotube formation and maturation, which are important factors for large-scale in vitro CM production that improve product quality, nutritional value, and efficacy. Full article

Background: The Neuro-2a cell line, derived from a murine neuroblastoma (NB), was established as early as 1969 and originates from a transplantable tumor that arose spontaneously in an A/Jax male mouse in 1940. Since then, it has been applied in over 10,000 studies and is used by the World Organization for Animal Health for the routine diagnosis of rabies. Surprisingly, however, Neuro-2a has never been genetically characterized in detail; this study fills that gap. Methods: The Neuro-2a cell line and two of its derivatives, Neuro-2a TR-alpha and Neuro-2a TR-beta, were analyzed for their chromosomal constitution using molecular cytogenetic approaches. Array comparative genomic hybridization was performed to characterize copy number alterations. Results: Neuro-2A has a hyper-tetraploid karyotype with 70 to 97 chromosomes per cell, and the karyotypes of its two examined derivatives were quite similar. Neither of them had a Y-chromosome. The complex karyotype of Neuro-2a includes mitotically stable dicentres, neocentrics, and complex rearrangements resembling chromothripsis events. Although no amplification of euchromatin or oncogenes was detected, there are five derivative chromosomes with the amplification of centromere-near heterochromatic material and 1–5 additional derivatives consisting only of such material. Conclusions: Since satellite DNA amplification has recently been found in advanced human tumors, this finding may be the corresponding equivalent in mice. An in silico translation of the obtained results into the human genome indicated that Neuro-2A is suitable as a model for advanced human NB. Full article

The monitoring of grape quality parameters within viticulture using airborne remote sensing is an increasingly important aspect of precision viticulture. Airborne remote sensing allows high volumes of spatial consistent data to be collected with improved efficiency over ground-based surveys. Spectral data can be used to understand the characteristics of vineyards, including the characteristics and health of the vines. Within viticultural remote sensing, the use of cover-crop spectra for monitoring is often overlooked due to the perceived noise it generates within imagery. However, within viticulture, the cover crop is a widely used and important management tool. This study uses multispectral data acquired by a high-resolution uncrewed aerial vehicle (UAV) and Sentinel-2 MSI to explore the benefit that cover-crop pixels could have for grape yield and quality monitoring. This study was undertaken across three growing seasons in the southeast of England, at a large commercial wine producer. The site was split into a number of vineyards, with sub-blocks for different vine varieties and rootstocks. Pre-harvest multispectral UAV imagery was collected across three vineyard parcels. UAV imagery was radiometrically corrected and stitched to create orthomosaics (red, green, and near-infrared) for each vineyard and survey date. Orthomosaics were segmented into pure cover-crop_uav and pure vine_uav pixels, removing the impact that mixed pixels could have upon analysis, with three vegetation indices (VIs) constructed from the segmented imagery. Sentinel-2 Level 2a bottom of atmosphere scenes were also acquired as close to UAV surveys as possible. In parallel, the yield and quality surveys were undertaken one to two weeks prior to harvest. Laboratory refractometry was performed to determine the grape total acid, total soluble solids, alpha amino acids, and berry weight. Extreme gradient boosting (XGBoost v2.1.1) was used to determine the ability of remote sensing data to predict the grape yield and quality parameters. Results suggested that pure cover-crop_uav was a successful predictor of grape yield and quality parameters (range of R² = 0.37–0.45), with model evaluation results comparable to pure vine_uav and Sentinel-2 models. The analysis also showed that, whilst the structural similarity between the both UAV and Sentinel-2 data was high, the cover crop is the most influential spectral component within the Sentinel-2 data. This research presents novel evidence for the ability of cover-crop_uav to predict grape yield and quality. Moreover, this finding then provides a mechanism which explains the success of the Sentinel-2 modelling of grape yield and quality. For growers and wine producers, creating grape yield and quality prediction models through moderate-resolution satellite imagery would be a significant innovation. Proving more cost-effective than UAV monitoring for large vineyards, such methodologies could also act to bring substantial cost savings to vineyard management. Full article

Forest fires are increasingly destructive, contributing to significant ecological damage, carbon emissions, and economic losses. Monitoring these fires promptly and accurately, particularly by delineating fire perimeters, is critical for mitigating their impact. Satellite-based remote sensing, especially using active fire products from VIIRS and MODIS, has proven indispensable for real-time forest fire monitoring. Despite advancements, challenges remain in accurately clustering and delineating fire perimeters in a timely manner, as many existing methods rely on manual processing, resulting in delays. Active fire perimeter (AFP) and Timely Active Fire Progression (TAFP) models were developed which aim to be an automated approach for clustering active fire data points and delineating perimeters. The results demonstrated that the combined dataset achieved the highest matching rate of 85.13% for fire perimeters across all size classes, with a 95.95% clustering accuracy for fires ≥100 ha. However, the accuracy decreased for smaller fires. Overall, 1500 m radii with alpha values of 0.1 were found to be the most effective for fire perimeter delineation, particularly when applied at larger radii. The proposed models can play a critical role in improving operational responses by fire management agencies, helping to mitigate the destructive impact of forest fires more effectively. Full article

From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite HORs in the centromere of orangutan chromosome 13, discovering a novel 59mer HOR—the longest HOR unit identified in any primate to date. Additionally, it revealed the first intertwined sequence of three HORs, 18mer/27mer/45mer HORs, with a common aligned “backbone” across all HOR copies. The major 7mer HOR exhibits a Willard’s-type canonical copy, although some segments of the array display significant irregularities. In contrast, the 14mer HOR forms a regular Willard’s-type HOR array. Surprisingly, the GRM2023 high-precision analysis of chromosome 13 of human genome assembly T2T-CHM13v2.0 reveals the presence of only a 7mer HOR, despite both the orangutan and human genome assemblies being derived from whole genome shotgun sequences. Full article

Wild edible plants, botanically defined as phytoalimurgical species, have historically been a useful source of food to cope with recurrent famines and poor farming conditions. If properly identified, harvested, transformed and promoted, alimurgical plants could further enhance the wellbeing of rural and urban communities and the multifunctional productivity of agriculture. The research aimed to survey alimurgical species in a wetland, map their location, detect their spatial richness, and develop a monitoring plan for ongoing vegetation succession. The study area is the King’s Lagoon, a wetland that has recently undergone a radical restoration of its natural layout. A satellite image was used to create a land cover map and interpret the relationship between plant species and land cover. The survey provided a snapshot of the wetland’s current ecosystem status and used botanical analysis and ecological indices to investigate biodiversity levels. The alpha, beta and gamma levels of biodiversity were explored and interpreted through the statistical processing of a comprehensive dataset of species occurrence and abundance, together with the calculation of Shannon’s, Simpson’s and Jaccard’s indices. It was observed that biodiversity in the wetland is developing gradually following restoration and is expected to increase over time as successional stages take hold. Biodiversity is more pronounced along the banks of the canals and watercourses connecting the basins and open ponds, while it is less pronounced in areas where the soil has been disturbed by previous excavations. Salicornia spp., Beta vulgaris subsp. maritima and Suaeda vera were identified as the most common and interesting species found in the study area. The potential for cultivation of some of the halophyte species that were monitored was also highlighted, with particular reference to the selection of the most commercially interesting species, the best species associations and intercropping practices in a wetland context, which must always prioritize the conservation of wild biodiversity. The spring surveys should be repeated in the coming years in order to accurately trace the dynamics of the ecological succession of this particular ecosystem, once it has returned to its natural development. Full article

Chromosomal translocations can result in phenotypic effects of varying severity, depending on the position of the breakpoints and the rearrangement of genes within the interphase nucleus of the translocated chromosome regions. Balanced translocations are often asymptomatic phenotypically and are typically detected due to a decrease in fertility resulting from issues during meiosis. Robertsonian translocations are among the most common chromosomal abnormalities, often asymptomatic, and can persist in the population as a normal polymorphism. We serendipitously discovered a Robertsonian translocation between chromosome 21 and chromosome 22, which is inherited across three generations without any phenotypic effect, notably only in females. In situ hybridization with alpha-satellite DNAs revealed the presence of both centromeric sequences in the translocated chromosome. The reciprocal translocation resulted in a partial deletion of the short arm of both chromosomes 21, and 22, with the ribosomal RNA genes remaining present in the middle part of the new metacentric chromosome. The rearrangement did not cause alterations to the long arm. The spread of an asymptomatic heterozygous chromosomal polymorphism in a population can lead to mating between heterozygous individuals, potentially resulting in offspring with a homozygous chromosomal configuration for the anomaly they carry. This new karyotype may not produce phenotypic effects in the individual who presents it. The frequency of karyotypes with chromosomal rearrangements in asymptomatic heterozygous form in human populations is likely underestimated, and molecular karyotype by array Comparative Genomic Hybridization (array-CGH) analysis does not allow for the identification of this type of chromosomal anomaly, making classical cytogenetic analysis the preferred method for obtaining clear results on a karyotype carrying a balanced rearrangement. Full article

Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension of genetic disorders and therapeutic interventions. This study rigorously identified and structurally analyzed alpha satellite higher-order repeats (HORs) within the centromere of human chromosome 15 in the complete T2T-CHM13 assembly using the high-precision GRM2023 algorithm. The most extensive alpha satellite HOR array in chromosome 15 reveals a novel cascading HOR, housing 429 15mer HOR copies, containing 4-, 7- and 11-monomer subfragments. Within each row of cascading HORs, all alpha satellite monomers are of distinct types, as in regular Willard’s HORs. However, different HOR copies within the same cascading 15mer HOR contain more than one monomer of the same type. Each canonical 15mer HOR copy comprises 15 monomers belonging to only 9 different monomer types. Notably, 65% of the 429 15mer cascading HOR copies exhibit canonical structures, while 35% display variant configurations. Identified as the second most extensive alpha satellite HOR, another novel cascading HOR within human chromosome 15 encompasses 164 20mer HOR copies, each featuring two subfragments. Moreover, a distinct pattern emerges as interspersed 25mer/26mer structures differing from regular Willard’s HORs and giving rise to a 34-monomer subfragment. Only a minor 18mer HOR array of 12 HOR copies is of the regular Willard’s type. These revelations highlight the complexity within the chromosome 15 centromeric region, accentuating deviations from anticipated highly regular patterns and hinting at profound information encoding and functional potential within the human centromere. Full article

Within the past decade, the aerospace engineering industry has evolved beyond the constraints of using single, large, custom satellites. Due to the increased reliability and robustness of commercial, off-the-shelf printed circuit board components, missions have instead transitioned towards deploying swarms of smaller satellites. Such an approach significantly decreases the mission cost by reducing custom engineering and deployment expenses. Nanosatellites can be quickly developed with a more modular design at lower risk. The Alpha mission at the Cornell University Space Systems Studio is fabricated in this manner. However, for the purpose of development, the initial proof of concept included a two-satellite system. The manuscript will discuss system engineering approaches used to model and mature the design of the pilot satellite. The two systems that will be primarily focused on are the attitude control system of the carrier nanosatellite and the radio frequency communications on the excreted femto-satellites. Milestones achieved include ChipSat to ChipSat communication, ChipSat to ground station communication, packet creation, error correction, appending a preamble, and filtering the signal. Other achievements include controller traceability/verification and validation, software rigidity tests, hardware endurance testing, Kane damper, and inertial measurement unit tuning. These developments matured the technological readiness level (TRL) of systems in preparation for satellite deployment. Full article